Starting phenix.real_space_refine on Wed Jul 30 12:57:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hyd_0308/07_2025/6hyd_0308.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hyd_0308/07_2025/6hyd_0308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hyd_0308/07_2025/6hyd_0308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hyd_0308/07_2025/6hyd_0308.map" model { file = "/net/cci-nas-00/data/ceres_data/6hyd_0308/07_2025/6hyd_0308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hyd_0308/07_2025/6hyd_0308.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 25 5.16 5 C 7883 2.51 5 N 2023 2.21 5 O 2237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12168 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1137, 8850 Classifications: {'peptide': 1137} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 1110} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 449 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 360 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 15, 'PHE:plan': 3, 'GLU:plan': 28, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 258 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 7, 'TRANS': 429} Chain breaks: 9 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'UNK:plan-1': 31, 'ASP:plan': 6, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 7.93, per 1000 atoms: 0.65 Number of scatterers: 12168 At special positions: 0 Unit cell: (171.6, 170.5, 121, 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 25 16.00 O 2237 8.00 N 2023 7.00 C 7883 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: 3.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 0 sheets defined 70.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 2358 through 2363 removed outlier: 3.573A pdb=" N ALA A2363 " --> pdb=" O GLU A2359 " (cutoff:3.500A) Processing helix chain 'A' and resid 2368 through 2373 removed outlier: 3.546A pdb=" N GLU A2372 " --> pdb=" O SER A2368 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL A2373 " --> pdb=" O HIS A2369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2368 through 2373' Processing helix chain 'A' and resid 2375 through 2381 Processing helix chain 'A' and resid 2391 through 2405 removed outlier: 3.818A pdb=" N TYR A2396 " --> pdb=" O ALA A2392 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A2405 " --> pdb=" O PHE A2401 " (cutoff:3.500A) Processing helix chain 'A' and resid 2406 through 2412 removed outlier: 3.507A pdb=" N ASN A2412 " --> pdb=" O LEU A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2415 through 2426 Processing helix chain 'A' and resid 2446 through 2451 Processing helix chain 'A' and resid 2462 through 2487 removed outlier: 4.467A pdb=" N LEU A2466 " --> pdb=" O SER A2462 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A2469 " --> pdb=" O LEU A2465 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A2470 " --> pdb=" O LEU A2466 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A2471 " --> pdb=" O SER A2467 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A2478 " --> pdb=" O ASN A2474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A2480 " --> pdb=" O LEU A2476 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A2482 " --> pdb=" O ALA A2478 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A2487 " --> pdb=" O ASN A2483 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2500 Processing helix chain 'A' and resid 2522 through 2532 removed outlier: 3.589A pdb=" N VAL A2527 " --> pdb=" O ASN A2523 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A2532 " --> pdb=" O MET A2528 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2547 Processing helix chain 'A' and resid 2549 through 2560 removed outlier: 3.509A pdb=" N ILE A2553 " --> pdb=" O ASP A2549 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A2555 " --> pdb=" O LEU A2551 " (cutoff:3.500A) Processing helix chain 'A' and resid 2565 through 2570 Processing helix chain 'A' and resid 2571 through 2576 removed outlier: 3.740A pdb=" N ILE A2576 " --> pdb=" O TYR A2572 " (cutoff:3.500A) Processing helix chain 'A' and resid 2577 through 2584 Processing helix chain 'A' and resid 2590 through 2595 removed outlier: 4.343A pdb=" N PHE A2594 " --> pdb=" O GLU A2590 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A2595 " --> pdb=" O ILE A2591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2590 through 2595' Processing helix chain 'A' and resid 2600 through 2606 removed outlier: 3.656A pdb=" N VAL A2604 " --> pdb=" O GLU A2600 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A2606 " --> pdb=" O THR A2602 " (cutoff:3.500A) Processing helix chain 'A' and resid 2612 through 2617 Processing helix chain 'A' and resid 2627 through 2649 removed outlier: 3.875A pdb=" N TRP A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A2632 " --> pdb=" O SER A2628 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A2633 " --> pdb=" O ASN A2629 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A2636 " --> pdb=" O LEU A2632 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A2638 " --> pdb=" O PHE A2634 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A2643 " --> pdb=" O ASN A2639 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A2645 " --> pdb=" O SER A2641 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A2646 " --> pdb=" O GLU A2642 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A2647 " --> pdb=" O LYS A2643 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A2649 " --> pdb=" O ASP A2645 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2674 removed outlier: 3.923A pdb=" N ASP A2664 " --> pdb=" O LYS A2660 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A2666 " --> pdb=" O LEU A2662 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG A2667 " --> pdb=" O MET A2663 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A2674 " --> pdb=" O ASN A2670 " (cutoff:3.500A) Processing helix chain 'A' and resid 2680 through 2700 removed outlier: 3.650A pdb=" N SER A2686 " --> pdb=" O ASN A2682 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A2687 " --> pdb=" O LEU A2683 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A2688 " --> pdb=" O LEU A2684 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A2699 " --> pdb=" O LEU A2695 " (cutoff:3.500A) Processing helix chain 'A' and resid 2710 through 2720 removed outlier: 3.520A pdb=" N PHE A2714 " --> pdb=" O PHE A2710 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A2715 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A2718 " --> pdb=" O PHE A2714 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG A2719 " --> pdb=" O ASP A2715 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR A2720 " --> pdb=" O ASN A2716 " (cutoff:3.500A) Processing helix chain 'A' and resid 2726 through 2733 removed outlier: 3.892A pdb=" N ILE A2730 " --> pdb=" O THR A2726 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A2731 " --> pdb=" O ALA A2727 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A2732 " --> pdb=" O GLU A2728 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2745 removed outlier: 3.540A pdb=" N LEU A2744 " --> pdb=" O ALA A2740 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A2745 " --> pdb=" O THR A2741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2740 through 2745' Processing helix chain 'A' and resid 2757 through 2762 removed outlier: 4.692A pdb=" N TRP A2762 " --> pdb=" O PHE A2758 " (cutoff:3.500A) Processing helix chain 'A' and resid 2779 through 2791 removed outlier: 3.604A pdb=" N ASP A2784 " --> pdb=" O GLN A2780 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A2786 " --> pdb=" O LEU A2782 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A2787 " --> pdb=" O GLU A2783 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A2791 " --> pdb=" O ARG A2787 " (cutoff:3.500A) Processing helix chain 'A' and resid 2806 through 2815 Processing helix chain 'A' and resid 2817 through 2823 removed outlier: 3.540A pdb=" N LEU A2822 " --> pdb=" O SER A2818 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A2823 " --> pdb=" O PRO A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2830 through 2838 removed outlier: 4.012A pdb=" N TRP A2836 " --> pdb=" O MET A2832 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A2838 " --> pdb=" O LEU A2834 " (cutoff:3.500A) Processing helix chain 'A' and resid 2839 through 2845 Processing helix chain 'A' and resid 2853 through 2860 removed outlier: 3.591A pdb=" N LEU A2857 " --> pdb=" O THR A2853 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS A2858 " --> pdb=" O LEU A2854 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A2860 " --> pdb=" O GLU A2856 " (cutoff:3.500A) Processing helix chain 'A' and resid 2860 through 2865 Processing helix chain 'A' and resid 2868 through 2874 removed outlier: 3.901A pdb=" N THR A2872 " --> pdb=" O GLU A2868 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A2874 " --> pdb=" O ARG A2870 " (cutoff:3.500A) Processing helix chain 'A' and resid 2878 through 2886 removed outlier: 4.051A pdb=" N ALA A2884 " --> pdb=" O ALA A2880 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A2885 " --> pdb=" O LEU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2889 through 2904 removed outlier: 3.554A pdb=" N LEU A2893 " --> pdb=" O SER A2889 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A2896 " --> pdb=" O GLU A2892 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A2898 " --> pdb=" O GLY A2894 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A2900 " --> pdb=" O ALA A2896 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A2904 " --> pdb=" O PHE A2900 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2923 removed outlier: 3.893A pdb=" N TYR A2921 " --> pdb=" O ALA A2917 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A2923 " --> pdb=" O HIS A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2924 through 2943 removed outlier: 3.665A pdb=" N SER A2934 " --> pdb=" O THR A2930 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A2941 " --> pdb=" O LEU A2937 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN A2943 " --> pdb=" O LYS A2939 " (cutoff:3.500A) Processing helix chain 'A' and resid 2944 through 2947 Processing helix chain 'A' and resid 2954 through 2960 removed outlier: 3.909A pdb=" N LYS A2958 " --> pdb=" O ILE A2954 " (cutoff:3.500A) Processing helix chain 'A' and resid 2980 through 2982 No H-bonds generated for 'chain 'A' and resid 2980 through 2982' Processing helix chain 'A' and resid 2983 through 2992 removed outlier: 3.583A pdb=" N GLU A2987 " --> pdb=" O SER A2983 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A2989 " --> pdb=" O PHE A2985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3009 removed outlier: 3.506A pdb=" N LYS A3002 " --> pdb=" O SER A2998 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A3003 " --> pdb=" O ARG A2999 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A3004 " --> pdb=" O GLN A3000 " (cutoff:3.500A) Processing helix chain 'A' and resid 3014 through 3033 removed outlier: 4.175A pdb=" N ARG A3018 " --> pdb=" O GLN A3014 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A3019 " --> pdb=" O SER A3015 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A3020 " --> pdb=" O ASP A3016 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET A3021 " --> pdb=" O ARG A3017 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A3027 " --> pdb=" O GLN A3023 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3069 removed outlier: 3.699A pdb=" N ILE A3046 " --> pdb=" O ASP A3042 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A3047 " --> pdb=" O LEU A3043 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A3050 " --> pdb=" O ILE A3046 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A3053 " --> pdb=" O GLY A3049 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A3054 " --> pdb=" O TYR A3050 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A3058 " --> pdb=" O ILE A3054 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A3061 " --> pdb=" O GLY A3057 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A3063 " --> pdb=" O ASP A3059 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN A3064 " --> pdb=" O LEU A3060 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A3067 " --> pdb=" O LEU A3063 " (cutoff:3.500A) Processing helix chain 'A' and resid 3087 through 3094 removed outlier: 3.815A pdb=" N LEU A3092 " --> pdb=" O ALA A3088 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3103 removed outlier: 3.677A pdb=" N LYS A3103 " --> pdb=" O SER A3099 " (cutoff:3.500A) Processing helix chain 'A' and resid 3111 through 3114 Processing helix chain 'A' and resid 3115 through 3124 removed outlier: 3.621A pdb=" N LEU A3120 " --> pdb=" O LEU A3116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A3121 " --> pdb=" O MET A3117 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A3124 " --> pdb=" O LEU A3120 " (cutoff:3.500A) Processing helix chain 'A' and resid 3133 through 3146 removed outlier: 4.312A pdb=" N ALA A3139 " --> pdb=" O ILE A3135 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A3140 " --> pdb=" O PHE A3136 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A3142 " --> pdb=" O ALA A3138 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A3143 " --> pdb=" O ALA A3139 " (cutoff:3.500A) Processing helix chain 'A' and resid 3149 through 3155 Processing helix chain 'A' and resid 3203 through 3207 removed outlier: 3.649A pdb=" N TYR A3207 " --> pdb=" O LEU A3203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3203 through 3207' Processing helix chain 'A' and resid 3211 through 3218 removed outlier: 4.339A pdb=" N PHE A3218 " --> pdb=" O TYR A3214 " (cutoff:3.500A) Processing helix chain 'A' and resid 3232 through 3241 removed outlier: 4.042A pdb=" N ILE A3236 " --> pdb=" O SER A3232 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A3237 " --> pdb=" O GLY A3233 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR A3238 " --> pdb=" O ALA A3234 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A3239 " --> pdb=" O ILE A3235 " (cutoff:3.500A) Processing helix chain 'A' and resid 3253 through 3269 removed outlier: 3.539A pdb=" N LEU A3257 " --> pdb=" O LYS A3253 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A3258 " --> pdb=" O SER A3254 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A3259 " --> pdb=" O GLY A3255 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A3260 " --> pdb=" O SER A3256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A3261 " --> pdb=" O LEU A3257 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN A3262 " --> pdb=" O SER A3258 " (cutoff:3.500A) Processing helix chain 'A' and resid 3287 through 3308 removed outlier: 4.317A pdb=" N LYS A3293 " --> pdb=" O PRO A3289 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A3299 " --> pdb=" O GLY A3295 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A3301 " --> pdb=" O ILE A3297 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A3304 " --> pdb=" O THR A3300 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A3306 " --> pdb=" O LEU A3302 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A3308 " --> pdb=" O SER A3304 " (cutoff:3.500A) Processing helix chain 'A' and resid 3316 through 3329 removed outlier: 3.877A pdb=" N TYR A3322 " --> pdb=" O LEU A3318 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A3329 " --> pdb=" O SER A3325 " (cutoff:3.500A) Processing helix chain 'A' and resid 3336 through 3358 removed outlier: 3.600A pdb=" N GLN A3340 " --> pdb=" O PRO A3336 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A3347 " --> pdb=" O LYS A3343 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A3348 " --> pdb=" O ILE A3344 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A3349 " --> pdb=" O GLU A3345 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A3356 " --> pdb=" O ALA A3352 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A3357 " --> pdb=" O GLU A3353 " (cutoff:3.500A) Processing helix chain 'A' and resid 3364 through 3388 removed outlier: 3.867A pdb=" N LEU A3370 " --> pdb=" O ASN A3366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A3380 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A3381 " --> pdb=" O SER A3377 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A3382 " --> pdb=" O TRP A3378 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A3385 " --> pdb=" O LEU A3381 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A3388 " --> pdb=" O ARG A3384 " (cutoff:3.500A) Processing helix chain 'A' and resid 3392 through 3397 Processing helix chain 'A' and resid 3404 through 3412 removed outlier: 3.745A pdb=" N GLU A3410 " --> pdb=" O PHE A3406 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A3411 " --> pdb=" O TYR A3407 " (cutoff:3.500A) Processing helix chain 'A' and resid 3412 through 3417 Processing helix chain 'A' and resid 3428 through 3441 removed outlier: 3.513A pdb=" N SER A3433 " --> pdb=" O THR A3429 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A3437 " --> pdb=" O SER A3433 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE A3438 " --> pdb=" O SER A3434 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A3439 " --> pdb=" O LEU A3435 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A3441 " --> pdb=" O LEU A3437 " (cutoff:3.500A) Processing helix chain 'A' and resid 3447 through 3463 removed outlier: 3.788A pdb=" N LEU A3453 " --> pdb=" O ALA A3449 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A3455 " --> pdb=" O LEU A3451 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA A3456 " --> pdb=" O ASP A3452 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS A3460 " --> pdb=" O ALA A3456 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A3461 " --> pdb=" O PHE A3457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A3462 " --> pdb=" O TYR A3458 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3484 removed outlier: 3.833A pdb=" N ASN A3477 " --> pdb=" O GLY A3473 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A3478 " --> pdb=" O LEU A3474 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A3479 " --> pdb=" O LEU A3475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A3482 " --> pdb=" O THR A3478 " (cutoff:3.500A) Processing helix chain 'A' and resid 3485 through 3511 removed outlier: 3.606A pdb=" N ASN A3495 " --> pdb=" O GLU A3491 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A3496 " --> pdb=" O ARG A3492 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A3498 " --> pdb=" O THR A3494 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A3499 " --> pdb=" O ASN A3495 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A3500 " --> pdb=" O GLY A3496 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A3502 " --> pdb=" O LYS A3498 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU A3503 " --> pdb=" O SER A3499 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A3507 " --> pdb=" O GLU A3503 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A3509 " --> pdb=" O ASP A3505 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A3511 " --> pdb=" O ILE A3507 " (cutoff:3.500A) Processing helix chain 'A' and resid 3517 through 3544 removed outlier: 3.514A pdb=" N LEU A3521 " --> pdb=" O ASN A3517 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A3522 " --> pdb=" O VAL A3518 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A3523 " --> pdb=" O ASP A3519 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A3526 " --> pdb=" O LYS A3522 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A3527 " --> pdb=" O GLN A3523 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A3528 " --> pdb=" O SER A3524 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A3531 " --> pdb=" O LYS A3527 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A3533 " --> pdb=" O HIS A3529 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS A3534 " --> pdb=" O ASN A3530 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A3535 " --> pdb=" O ASN A3531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A3541 " --> pdb=" O ARG A3537 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A3542 " --> pdb=" O LYS A3538 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A3543 " --> pdb=" O TYR A3539 " (cutoff:3.500A) Processing helix chain 'A' and resid 3547 through 3554 removed outlier: 3.711A pdb=" N ILE A3551 " --> pdb=" O ALA A3547 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A3554 " --> pdb=" O ILE A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3586 removed outlier: 3.754A pdb=" N UNK A3584 " --> pdb=" O UNK A3580 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N UNK A3585 " --> pdb=" O UNK A3581 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3617 removed outlier: 3.716A pdb=" N ASN A3607 " --> pdb=" O THR A3603 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A3609 " --> pdb=" O ALA A3605 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A3613 " --> pdb=" O ASP A3609 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A3614 " --> pdb=" O SER A3610 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A3615 " --> pdb=" O TYR A3611 " (cutoff:3.500A) Processing helix chain 'A' and resid 3623 through 3640 removed outlier: 3.679A pdb=" N PHE A3630 " --> pdb=" O LEU A3626 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A3640 " --> pdb=" O ARG A3636 " (cutoff:3.500A) Processing helix chain 'A' and resid 3653 through 3674 removed outlier: 3.589A pdb=" N THR A3658 " --> pdb=" O ALA A3654 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A3659 " --> pdb=" O TYR A3655 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A3663 " --> pdb=" O GLN A3659 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A3668 " --> pdb=" O LEU A3664 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3690 through 3695 removed outlier: 3.684A pdb=" N ILE A3694 " --> pdb=" O SER A3690 " (cutoff:3.500A) Processing helix chain 'A' and resid 3706 through 3712 removed outlier: 3.594A pdb=" N ASP A3710 " --> pdb=" O ASN A3707 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE A3712 " --> pdb=" O SER A3709 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3727 removed outlier: 3.629A pdb=" N ARG A3724 " --> pdb=" O LEU A3720 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A3726 " --> pdb=" O LYS A3722 " (cutoff:3.500A) Processing helix chain 'A' and resid 3737 through 3755 removed outlier: 3.666A pdb=" N ALA A3744 " --> pdb=" O GLU A3740 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A3747 " --> pdb=" O MET A3743 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A3748 " --> pdb=" O ALA A3744 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A3749 " --> pdb=" O LEU A3745 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A3755 " --> pdb=" O PHE A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3756 through 3780 removed outlier: 3.521A pdb=" N CYS A3768 " --> pdb=" O THR A3764 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A3769 " --> pdb=" O ASN A3765 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A3775 " --> pdb=" O ASN A3771 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A3776 " --> pdb=" O GLY A3772 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A3779 " --> pdb=" O LEU A3775 " (cutoff:3.500A) Processing helix chain 'A' and resid 3792 through 3805 removed outlier: 3.665A pdb=" N ASP A3797 " --> pdb=" O LYS A3793 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A3798 " --> pdb=" O ALA A3794 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A3802 " --> pdb=" O ASN A3798 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A3804 " --> pdb=" O ARG A3800 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP A3805 " --> pdb=" O LEU A3801 " (cutoff:3.500A) Processing helix chain 'A' and resid 3805 through 3822 removed outlier: 3.772A pdb=" N ASP A3811 " --> pdb=" O PRO A3807 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A3815 " --> pdb=" O ASP A3811 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A3816 " --> pdb=" O TYR A3812 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A3817 " --> pdb=" O ALA A3813 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER A3818 " --> pdb=" O ALA A3814 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A3822 " --> pdb=" O SER A3818 " (cutoff:3.500A) Processing helix chain 'A' and resid 3827 through 3829 No H-bonds generated for 'chain 'A' and resid 3827 through 3829' Processing helix chain 'A' and resid 3830 through 3839 removed outlier: 4.037A pdb=" N ALA A3836 " --> pdb=" O ILE A3832 " (cutoff:3.500A) Processing helix chain 'A' and resid 3840 through 3845 removed outlier: 3.976A pdb=" N VAL A3845 " --> pdb=" O SER A3841 " (cutoff:3.500A) Processing helix chain 'A' and resid 3854 through 3856 No H-bonds generated for 'chain 'A' and resid 3854 through 3856' Processing helix chain 'A' and resid 3857 through 3878 removed outlier: 4.342A pdb=" N ARG A3863 " --> pdb=" O GLU A3859 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A3869 " --> pdb=" O GLU A3865 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A3876 " --> pdb=" O LEU A3872 " (cutoff:3.500A) Processing helix chain 'A' and resid 3884 through 3898 removed outlier: 4.315A pdb=" N ILE A3889 " --> pdb=" O PHE A3885 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE A3890 " --> pdb=" O VAL A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3925 removed outlier: 3.628A pdb=" N THR A3922 " --> pdb=" O ALA A3918 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE A3923 " --> pdb=" O PHE A3919 " (cutoff:3.500A) Processing helix chain 'A' and resid 3927 through 3936 removed outlier: 3.625A pdb=" N LYS A3932 " --> pdb=" O LEU A3928 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A3933 " --> pdb=" O SER A3929 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A3934 " --> pdb=" O PHE A3930 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP A3936 " --> pdb=" O LYS A3932 " (cutoff:3.500A) Processing helix chain 'A' and resid 3948 through 3964 removed outlier: 3.528A pdb=" N SER A3952 " --> pdb=" O TRP A3948 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A3953 " --> pdb=" O LEU A3949 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A3954 " --> pdb=" O SER A3950 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET A3957 " --> pdb=" O PHE A3953 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A3961 " --> pdb=" O MET A3957 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A3963 " --> pdb=" O ASN A3959 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A3964 " --> pdb=" O VAL A3960 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3981 removed outlier: 3.533A pdb=" N SER A3969 " --> pdb=" O SER A3965 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A3970 " --> pdb=" O SER A3966 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU A3973 " --> pdb=" O SER A3969 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A3978 " --> pdb=" O THR A3974 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A3979 " --> pdb=" O ALA A3975 " (cutoff:3.500A) Processing helix chain 'A' and resid 3992 through 3997 removed outlier: 3.737A pdb=" N SER A3997 " --> pdb=" O LYS A3993 " (cutoff:3.500A) Processing helix chain 'A' and resid 3999 through 4007 removed outlier: 3.566A pdb=" N ILE A4003 " --> pdb=" O THR A3999 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A4005 " --> pdb=" O PRO A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4041 removed outlier: 3.872A pdb=" N VAL A4013 " --> pdb=" O ALA A4009 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A4015 " --> pdb=" O THR A4011 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A4021 " --> pdb=" O SER A4017 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A4026 " --> pdb=" O THR A4022 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A4033 " --> pdb=" O TYR A4029 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A4034 " --> pdb=" O ILE A4030 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1368 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: 3.46 Time building geometry restraints manager: 3.56 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: 3790 1.34 - 1.46: 2200 1.46 - 1.57: 6358 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 12393 Sorted by residual: bond pdb=" C LEU A4000 " pdb=" N PRO A4001 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.29e+00 bond pdb=" C TRP A3312 " pdb=" N PRO A3313 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.26e+00 bond pdb=" N GLU A3988 " pdb=" CA GLU A3988 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.87e+00 bond pdb=" N PRO A2755 " pdb=" CA PRO A2755 " ideal model delta sigma weight residual 1.465 1.504 -0.039 2.03e-02 2.43e+03 3.66e+00 bond pdb=" C SER A2459 " pdb=" N PRO A2460 " ideal model delta sigma weight residual 1.337 1.354 -0.017 9.80e-03 1.04e+04 3.02e+00 ... (remaining 12388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 16538 2.79 - 5.58: 201 5.58 - 8.37: 45 8.37 - 11.15: 4 11.15 - 13.94: 6 Bond angle restraints: 16794 Sorted by residual: angle pdb=" C TYR A2445 " pdb=" N VAL A2446 " pdb=" CA VAL A2446 " ideal model delta sigma weight residual 121.97 133.38 -11.41 1.80e+00 3.09e-01 4.02e+01 angle pdb=" N VAL A2446 " pdb=" CA VAL A2446 " pdb=" C VAL A2446 " ideal model delta sigma weight residual 109.34 121.48 -12.14 2.08e+00 2.31e-01 3.41e+01 angle pdb=" C ASN A2753 " pdb=" N TYR A2754 " pdb=" CA TYR A2754 " ideal model delta sigma weight residual 121.80 135.74 -13.94 2.44e+00 1.68e-01 3.27e+01 angle pdb=" C PRO A3642 " pdb=" N ASN A3643 " pdb=" CA ASN A3643 " ideal model delta sigma weight residual 122.46 129.24 -6.78 1.41e+00 5.03e-01 2.31e+01 angle pdb=" C ILE A2515 " pdb=" N PRO A2516 " pdb=" CA PRO A2516 " ideal model delta sigma weight residual 119.84 125.59 -5.75 1.25e+00 6.40e-01 2.12e+01 ... (remaining 16789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 7078 15.25 - 30.50: 273 30.50 - 45.75: 63 45.75 - 61.00: 3 61.00 - 76.26: 4 Dihedral angle restraints: 7421 sinusoidal: 2735 harmonic: 4686 Sorted by residual: dihedral pdb=" CA TRP A3312 " pdb=" C TRP A3312 " pdb=" N PRO A3313 " pdb=" CA PRO A3313 " ideal model delta harmonic sigma weight residual -180.00 -133.45 -46.55 0 5.00e+00 4.00e-02 8.67e+01 dihedral pdb=" CA TYR A2445 " pdb=" C TYR A2445 " pdb=" N VAL A2446 " pdb=" CA VAL A2446 " ideal model delta harmonic sigma weight residual -180.00 -134.93 -45.07 0 5.00e+00 4.00e-02 8.13e+01 dihedral pdb=" CA ASP A3515 " pdb=" C ASP A3515 " pdb=" N VAL A3516 " pdb=" CA VAL A3516 " ideal model delta harmonic sigma weight residual 180.00 -147.71 -32.29 0 5.00e+00 4.00e-02 4.17e+01 ... (remaining 7418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1526 0.053 - 0.105: 397 0.105 - 0.158: 49 0.158 - 0.211: 12 0.211 - 0.264: 2 Chirality restraints: 1986 Sorted by residual: chirality pdb=" CB ILE A2948 " pdb=" CA ILE A2948 " pdb=" CG1 ILE A2948 " pdb=" CG2 ILE A2948 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE A2613 " pdb=" CA ILE A2613 " pdb=" CG1 ILE A2613 " pdb=" CG2 ILE A2613 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA TRP A3312 " pdb=" N TRP A3312 " pdb=" C TRP A3312 " pdb=" CB TRP A3312 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1983 not shown) Planarity restraints: 2083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A3312 " -0.056 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A3313 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A3313 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A3313 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A2878 " 0.044 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO A2879 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A2879 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A2879 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A3081 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO A3082 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A3082 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A3082 " -0.033 5.00e-02 4.00e+02 ... (remaining 2080 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3878 2.83 - 3.35: 10539 3.35 - 3.87: 17569 3.87 - 4.38: 20673 4.38 - 4.90: 34371 Nonbonded interactions: 87030 Sorted by model distance: nonbonded pdb=" O ARG A2945 " pdb=" OG SER A2949 " model vdw 2.319 3.040 nonbonded pdb=" OG SER A3952 " pdb=" OH TYR A4020 " model vdw 2.320 3.040 nonbonded pdb=" O ILE A2861 " pdb=" OG1 THR A2865 " model vdw 2.325 3.040 nonbonded pdb=" OG SER A3929 " pdb=" O LEU A3963 " model vdw 2.359 3.040 nonbonded pdb=" OD1 ASN A3947 " pdb=" OG SER A3950 " model vdw 2.370 3.040 ... (remaining 87025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.360 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 0.004 0.054 12393 Z= 0.182 Angle : 0.852 13.943 16794 Z= 0.456 Chirality : 0.047 0.264 1986 Planarity : 0.006 0.086 2083 Dihedral : 9.332 76.256 4355 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.74 % Favored : 94.00 % Rotamer: Outliers : 0.24 % Allowed : 1.44 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.69 (0.12), residues: 1517 helix: -4.76 (0.05), residues: 1015 sheet: None (None), residues: 0 loop : -3.14 (0.22), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A2836 HIS 0.008 0.001 HIS A2844 PHE 0.026 0.002 PHE A2594 TYR 0.015 0.001 TYR A2709 ARG 0.005 0.001 ARG A2470 Details of bonding type rmsd hydrogen bonds : bond 0.34306 ( 466) hydrogen bonds : angle 9.49627 ( 1368) covalent geometry : bond 0.00373 (12393) covalent geometry : angle 0.85181 (16794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 325 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 2520 ILE cc_start: 0.6696 (mt) cc_final: 0.6471 (tp) REVERT: A 2684 LEU cc_start: 0.7613 (mt) cc_final: 0.7235 (tt) REVERT: A 2935 GLN cc_start: 0.7062 (mm110) cc_final: 0.6783 (mt0) REVERT: A 2939 LYS cc_start: 0.7436 (mmtp) cc_final: 0.6999 (pptt) REVERT: A 3245 LYS cc_start: 0.6239 (mmmt) cc_final: 0.5847 (ptmt) REVERT: A 3416 ASN cc_start: 0.7793 (t0) cc_final: 0.7435 (t0) REVERT: A 3507 ILE cc_start: 0.7854 (tt) cc_final: 0.7641 (mt) REVERT: A 3656 LEU cc_start: 0.7686 (tp) cc_final: 0.7329 (tp) outliers start: 3 outliers final: 0 residues processed: 327 average time/residue: 0.2581 time to fit residues: 117.7441 Evaluate side-chains 144 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 79 optimal weight: 0.0270 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2379 ASN A2598 ASN A2676 ASN A2716 ASN A2844 HIS A3222 HIS A3315 HIS ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3462 GLN A3484 GLN A3529 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125130 restraints weight = 16349.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126083 restraints weight = 14617.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126524 restraints weight = 12423.146| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12393 Z= 0.158 Angle : 0.666 12.031 16794 Z= 0.348 Chirality : 0.041 0.199 1986 Planarity : 0.005 0.081 2083 Dihedral : 5.470 47.347 1676 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.13 % Favored : 93.67 % Rotamer: Outliers : 3.21 % Allowed : 8.98 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.16), residues: 1517 helix: -3.12 (0.11), residues: 1008 sheet: None (None), residues: 0 loop : -2.83 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2836 HIS 0.003 0.001 HIS A3529 PHE 0.018 0.002 PHE A2601 TYR 0.013 0.001 TYR A2496 ARG 0.007 0.001 ARG A3398 Details of bonding type rmsd hydrogen bonds : bond 0.05496 ( 466) hydrogen bonds : angle 4.82487 ( 1368) covalent geometry : bond 0.00356 (12393) covalent geometry : angle 0.66572 (16794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 2466 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8075 (tp) REVERT: A 2520 ILE cc_start: 0.7156 (mt) cc_final: 0.6750 (tp) REVERT: A 2684 LEU cc_start: 0.7677 (mt) cc_final: 0.7198 (tt) REVERT: A 2703 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7786 (mp) REVERT: A 2795 PHE cc_start: 0.8259 (m-80) cc_final: 0.8045 (m-80) REVERT: A 2892 GLU cc_start: 0.6673 (tt0) cc_final: 0.6465 (tt0) REVERT: A 2921 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7312 (m-80) REVERT: A 2941 TRP cc_start: 0.6539 (t60) cc_final: 0.6084 (t-100) REVERT: A 3229 GLU cc_start: 0.8458 (tp30) cc_final: 0.8096 (tp30) REVERT: A 3245 LYS cc_start: 0.6475 (mmmt) cc_final: 0.5915 (ptmt) REVERT: A 3741 ARG cc_start: 0.7171 (tpp80) cc_final: 0.6167 (tpt170) REVERT: A 3743 MET cc_start: 0.8270 (tpp) cc_final: 0.8063 (mmm) REVERT: A 3750 MET cc_start: 0.8079 (tpp) cc_final: 0.7737 (tpp) REVERT: A 3818 SER cc_start: 0.8012 (m) cc_final: 0.7732 (t) REVERT: A 4028 MET cc_start: 0.8023 (tpp) cc_final: 0.7817 (tpp) outliers start: 40 outliers final: 22 residues processed: 181 average time/residue: 0.2265 time to fit residues: 60.5733 Evaluate side-chains 150 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2403 THR Chi-restraints excluded: chain A residue 2466 LEU Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2686 SER Chi-restraints excluded: chain A residue 2697 LEU Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2883 LEU Chi-restraints excluded: chain A residue 2921 TYR Chi-restraints excluded: chain A residue 2932 THR Chi-restraints excluded: chain A residue 2994 SER Chi-restraints excluded: chain A residue 3241 SER Chi-restraints excluded: chain A residue 3502 LYS Chi-restraints excluded: chain A residue 3514 LYS Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3687 VAL Chi-restraints excluded: chain A residue 3702 ASN Chi-restraints excluded: chain A residue 3705 TYR Chi-restraints excluded: chain A residue 3781 THR Chi-restraints excluded: chain A residue 3797 ASP Chi-restraints excluded: chain A residue 3868 ILE Chi-restraints excluded: chain A residue 3925 SER Chi-restraints excluded: chain A residue 3934 ILE Chi-restraints excluded: chain A residue 4017 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 113 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2611 HIS A2716 ASN A3011 ASN ** A3340 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 = 0.3681 r_free = 0.3681 target = 0.143656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126243 restraints weight = 16804.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126972 restraints weight = 14273.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127337 restraints weight = 12905.352| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12393 Z= 0.170 Angle : 0.647 12.018 16794 Z= 0.334 Chirality : 0.042 0.190 1986 Planarity : 0.004 0.083 2083 Dihedral : 5.314 44.967 1676 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.06 % Favored : 93.74 % Rotamer: Outliers : 3.69 % Allowed : 11.31 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.18), residues: 1517 helix: -2.18 (0.14), residues: 1016 sheet: None (None), residues: 0 loop : -2.75 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2836 HIS 0.003 0.001 HIS A3789 PHE 0.018 0.002 PHE A2398 TYR 0.014 0.001 TYR A2752 ARG 0.006 0.001 ARG A3636 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 466) hydrogen bonds : angle 4.38007 ( 1368) covalent geometry : bond 0.00394 (12393) covalent geometry : angle 0.64655 (16794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 1.782 Fit side-chains revert: symmetry clash REVERT: A 2466 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8008 (tp) REVERT: A 2520 ILE cc_start: 0.7106 (mt) cc_final: 0.6726 (tp) REVERT: A 2629 ASN cc_start: 0.7191 (t0) cc_final: 0.6884 (t0) REVERT: A 2684 LEU cc_start: 0.7641 (mt) cc_final: 0.7236 (tt) REVERT: A 2795 PHE cc_start: 0.8511 (m-80) cc_final: 0.8175 (m-80) REVERT: A 2873 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8481 (t80) REVERT: A 2921 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: A 3152 PHE cc_start: 0.7483 (t80) cc_final: 0.7219 (t80) REVERT: A 3245 LYS cc_start: 0.6771 (mmmt) cc_final: 0.6055 (ptmt) REVERT: A 3410 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7872 (tm-30) REVERT: A 3705 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.6687 (t80) outliers start: 46 outliers final: 28 residues processed: 159 average time/residue: 0.2167 time to fit residues: 53.3488 Evaluate side-chains 136 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2381 LEU Chi-restraints excluded: chain A residue 2403 THR Chi-restraints excluded: chain A residue 2466 LEU Chi-restraints excluded: chain A residue 2583 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2697 LEU Chi-restraints excluded: chain A residue 2873 PHE Chi-restraints excluded: chain A residue 2883 LEU Chi-restraints excluded: chain A residue 2921 TYR Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 2994 SER Chi-restraints excluded: chain A residue 3149 VAL Chi-restraints excluded: chain A residue 3241 SER Chi-restraints excluded: chain A residue 3286 PHE Chi-restraints excluded: chain A residue 3305 VAL Chi-restraints excluded: chain A residue 3321 LEU Chi-restraints excluded: chain A residue 3366 ASN Chi-restraints excluded: chain A residue 3502 LYS Chi-restraints excluded: chain A residue 3514 LYS Chi-restraints excluded: chain A residue 3625 ASP Chi-restraints excluded: chain A residue 3693 THR Chi-restraints excluded: chain A residue 3702 ASN Chi-restraints excluded: chain A residue 3705 TYR Chi-restraints excluded: chain A residue 3781 THR Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3868 ILE Chi-restraints excluded: chain A residue 3925 SER Chi-restraints excluded: chain A residue 3927 ILE Chi-restraints excluded: chain A residue 3934 ILE Chi-restraints excluded: chain A residue 3964 ARG Chi-restraints excluded: chain A residue 4002 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 0.0060 chunk 134 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2716 ASN A3011 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127382 restraints weight = 16666.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127434 restraints weight = 14601.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127698 restraints weight = 12783.150| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12393 Z= 0.143 Angle : 0.598 12.473 16794 Z= 0.308 Chirality : 0.041 0.187 1986 Planarity : 0.004 0.083 2083 Dihedral : 5.095 42.975 1676 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.00 % Favored : 93.80 % Rotamer: Outliers : 3.37 % Allowed : 12.67 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.20), residues: 1517 helix: -1.59 (0.15), residues: 1021 sheet: None (None), residues: 0 loop : -2.59 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2836 HIS 0.002 0.000 HIS A3789 PHE 0.012 0.001 PHE A3058 TYR 0.012 0.001 TYR A2522 ARG 0.003 0.000 ARG A3398 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 466) hydrogen bonds : angle 4.05627 ( 1368) covalent geometry : bond 0.00333 (12393) covalent geometry : angle 0.59818 (16794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 2365 ILE cc_start: 0.1475 (OUTLIER) cc_final: 0.1170 (mt) REVERT: A 2520 ILE cc_start: 0.7145 (mt) cc_final: 0.6727 (tp) REVERT: A 2629 ASN cc_start: 0.7416 (t0) cc_final: 0.7103 (t0) REVERT: A 2684 LEU cc_start: 0.7591 (mt) cc_final: 0.7259 (tt) REVERT: A 2733 LEU cc_start: 0.8133 (mp) cc_final: 0.7912 (mp) REVERT: A 2873 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8433 (t80) REVERT: A 2921 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: A 3245 LYS cc_start: 0.6716 (mmmt) cc_final: 0.6082 (ptmt) REVERT: A 3410 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 3705 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.6886 (t80) outliers start: 42 outliers final: 31 residues processed: 142 average time/residue: 0.2333 time to fit residues: 50.2809 Evaluate side-chains 138 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2381 LEU Chi-restraints excluded: chain A residue 2403 THR Chi-restraints excluded: chain A residue 2583 VAL Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2686 SER Chi-restraints excluded: chain A residue 2697 LEU Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2859 SER Chi-restraints excluded: chain A residue 2873 PHE Chi-restraints excluded: chain A residue 2883 LEU Chi-restraints excluded: chain A residue 2921 TYR Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3149 VAL Chi-restraints excluded: chain A residue 3203 LEU Chi-restraints excluded: chain A residue 3204 ASP Chi-restraints excluded: chain A residue 3241 SER Chi-restraints excluded: chain A residue 3286 PHE Chi-restraints excluded: chain A residue 3342 GLN Chi-restraints excluded: chain A residue 3474 LEU Chi-restraints excluded: chain A residue 3502 LYS Chi-restraints excluded: chain A residue 3514 LYS Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3625 ASP Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3702 ASN Chi-restraints excluded: chain A residue 3705 TYR Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3834 LEU Chi-restraints excluded: chain A residue 3868 ILE Chi-restraints excluded: chain A residue 3925 SER Chi-restraints excluded: chain A residue 3934 ILE Chi-restraints excluded: chain A residue 3964 ARG Chi-restraints excluded: chain A residue 4002 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 40 optimal weight: 0.0470 chunk 151 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 145 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2651 GLN A2716 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126050 restraints weight = 16684.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126036 restraints weight = 15334.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126328 restraints weight = 13896.585| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12393 Z= 0.139 Angle : 0.584 11.820 16794 Z= 0.302 Chirality : 0.040 0.185 1986 Planarity : 0.004 0.083 2083 Dihedral : 4.966 40.727 1676 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.93 % Favored : 93.87 % Rotamer: Outliers : 4.81 % Allowed : 12.11 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.21), residues: 1517 helix: -1.19 (0.16), residues: 1022 sheet: None (None), residues: 0 loop : -2.55 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2836 HIS 0.002 0.001 HIS A3789 PHE 0.011 0.001 PHE A3058 TYR 0.011 0.001 TYR A2754 ARG 0.005 0.000 ARG A3636 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 466) hydrogen bonds : angle 3.87883 ( 1368) covalent geometry : bond 0.00322 (12393) covalent geometry : angle 0.58434 (16794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 113 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 2365 ILE cc_start: 0.1536 (OUTLIER) cc_final: 0.1304 (mp) REVERT: A 2466 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7999 (tp) REVERT: A 2520 ILE cc_start: 0.7190 (mt) cc_final: 0.6800 (tp) REVERT: A 2629 ASN cc_start: 0.7412 (t0) cc_final: 0.7153 (t0) REVERT: A 2684 LEU cc_start: 0.7557 (mt) cc_final: 0.7232 (tt) REVERT: A 2873 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8377 (t80) REVERT: A 2921 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: A 2933 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8156 (m-10) REVERT: A 3117 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: A 3245 LYS cc_start: 0.6739 (mmmt) cc_final: 0.6106 (ptmt) REVERT: A 3410 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7948 (tm-30) REVERT: A 3705 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.6979 (t80) outliers start: 60 outliers final: 36 residues processed: 161 average time/residue: 0.2159 time to fit residues: 53.5711 Evaluate side-chains 148 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2381 LEU Chi-restraints excluded: chain A residue 2466 LEU Chi-restraints excluded: chain A residue 2583 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2686 SER Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2873 PHE Chi-restraints excluded: chain A residue 2883 LEU Chi-restraints excluded: chain A residue 2921 TYR Chi-restraints excluded: chain A residue 2933 PHE Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3117 MET Chi-restraints excluded: chain A residue 3149 VAL Chi-restraints excluded: chain A residue 3203 LEU Chi-restraints excluded: chain A residue 3204 ASP Chi-restraints excluded: chain A residue 3241 SER Chi-restraints excluded: chain A residue 3286 PHE Chi-restraints excluded: chain A residue 3305 VAL Chi-restraints excluded: chain A residue 3321 LEU Chi-restraints excluded: chain A residue 3333 ILE Chi-restraints excluded: chain A residue 3342 GLN Chi-restraints excluded: chain A residue 3366 ASN Chi-restraints excluded: chain A residue 3474 LEU Chi-restraints excluded: chain A residue 3502 LYS Chi-restraints excluded: chain A residue 3514 LYS Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3625 ASP Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3693 THR Chi-restraints excluded: chain A residue 3702 ASN Chi-restraints excluded: chain A residue 3705 TYR Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3834 LEU Chi-restraints excluded: chain A residue 3868 ILE Chi-restraints excluded: chain A residue 3889 ILE Chi-restraints excluded: chain A residue 3925 SER Chi-restraints excluded: chain A residue 3927 ILE Chi-restraints excluded: chain A residue 3934 ILE Chi-restraints excluded: chain A residue 4002 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 80 optimal weight: 0.0370 chunk 155 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2716 ASN ** A3340 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 = 0.3709 r_free = 0.3709 target = 0.145052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137231 restraints weight = 16821.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130691 restraints weight = 34582.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129404 restraints weight = 25907.746| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12393 Z= 0.134 Angle : 0.581 11.172 16794 Z= 0.298 Chirality : 0.040 0.183 1986 Planarity : 0.004 0.083 2083 Dihedral : 4.905 42.993 1676 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.80 % Favored : 94.00 % Rotamer: Outliers : 3.69 % Allowed : 13.47 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.21), residues: 1517 helix: -0.90 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -2.45 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2836 HIS 0.003 0.001 HIS A3529 PHE 0.011 0.001 PHE A3056 TYR 0.012 0.001 TYR A2445 ARG 0.004 0.000 ARG A2976 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 466) hydrogen bonds : angle 3.80856 ( 1368) covalent geometry : bond 0.00311 (12393) covalent geometry : angle 0.58089 (16794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 2365 ILE cc_start: 0.1499 (OUTLIER) cc_final: 0.1238 (mp) REVERT: A 2466 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7963 (tp) REVERT: A 2520 ILE cc_start: 0.7145 (mt) cc_final: 0.6776 (tp) REVERT: A 2629 ASN cc_start: 0.7498 (t0) cc_final: 0.7251 (t0) REVERT: A 2684 LEU cc_start: 0.7499 (mt) cc_final: 0.7186 (tt) REVERT: A 2873 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8321 (t80) REVERT: A 2921 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: A 2933 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8225 (m-10) REVERT: A 3245 LYS cc_start: 0.6723 (mmmt) cc_final: 0.6089 (ptmt) REVERT: A 3410 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 3705 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7085 (t80) REVERT: A 3750 MET cc_start: 0.8097 (tpp) cc_final: 0.7819 (tpp) outliers start: 46 outliers final: 36 residues processed: 143 average time/residue: 0.2137 time to fit residues: 47.0533 Evaluate side-chains 141 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2381 LEU Chi-restraints excluded: chain A residue 2466 LEU Chi-restraints excluded: chain A residue 2583 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2686 SER Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2859 SER Chi-restraints excluded: chain A residue 2873 PHE Chi-restraints excluded: chain A residue 2883 LEU Chi-restraints excluded: chain A residue 2921 TYR Chi-restraints excluded: chain A residue 2933 PHE Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 3060 LEU Chi-restraints excluded: chain A residue 3149 VAL Chi-restraints excluded: chain A residue 3203 LEU Chi-restraints excluded: chain A residue 3204 ASP Chi-restraints excluded: chain A residue 3241 SER Chi-restraints excluded: chain A residue 3286 PHE Chi-restraints excluded: chain A residue 3321 LEU Chi-restraints excluded: chain A residue 3333 ILE Chi-restraints excluded: chain A residue 3342 GLN Chi-restraints excluded: chain A residue 3474 LEU Chi-restraints excluded: chain A residue 3502 LYS Chi-restraints excluded: chain A residue 3514 LYS Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3625 ASP Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3693 THR Chi-restraints excluded: chain A residue 3702 ASN Chi-restraints excluded: chain A residue 3705 TYR Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3834 LEU Chi-restraints excluded: chain A residue 3868 ILE Chi-restraints excluded: chain A residue 3889 ILE Chi-restraints excluded: chain A residue 3925 SER Chi-restraints excluded: chain A residue 3927 ILE Chi-restraints excluded: chain A residue 3934 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 151 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 74 optimal weight: 0.0980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2716 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137703 restraints weight = 16793.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131367 restraints weight = 33414.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.130303 restraints weight = 27076.669| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12393 Z= 0.123 Angle : 0.560 10.900 16794 Z= 0.289 Chirality : 0.040 0.180 1986 Planarity : 0.004 0.083 2083 Dihedral : 4.771 41.743 1676 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.87 % Favored : 93.94 % Rotamer: Outliers : 4.25 % Allowed : 13.87 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.21), residues: 1517 helix: -0.60 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -2.39 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A3354 HIS 0.002 0.000 HIS A3789 PHE 0.025 0.001 PHE A2398 TYR 0.012 0.001 TYR A2754 ARG 0.008 0.000 ARG A3636 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 466) hydrogen bonds : angle 3.67373 ( 1368) covalent geometry : bond 0.00283 (12393) covalent geometry : angle 0.55965 (16794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 104 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 2365 ILE cc_start: 0.1535 (OUTLIER) cc_final: 0.1292 (mt) REVERT: A 2466 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 2520 ILE cc_start: 0.7104 (mt) cc_final: 0.6767 (tp) REVERT: A 2684 LEU cc_start: 0.7466 (mt) cc_final: 0.7192 (tt) REVERT: A 2921 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: A 2958 LYS cc_start: 0.7136 (tppt) cc_final: 0.6850 (mtmm) REVERT: A 2975 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.5090 (p90) REVERT: A 3205 ASP cc_start: 0.8187 (t0) cc_final: 0.7938 (t0) REVERT: A 3245 LYS cc_start: 0.6717 (mmmt) cc_final: 0.6010 (ptmt) REVERT: A 3410 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 3705 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7090 (t80) REVERT: A 3868 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8421 (tp) REVERT: A 3892 GLU cc_start: 0.8080 (tp30) cc_final: 0.7841 (tp30) outliers start: 53 outliers final: 35 residues processed: 146 average time/residue: 0.2675 time to fit residues: 61.7993 Evaluate side-chains 138 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2381 LEU Chi-restraints excluded: chain A residue 2466 LEU Chi-restraints excluded: chain A residue 2583 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2686 SER Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2859 SER Chi-restraints excluded: chain A residue 2921 TYR Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 2975 TYR Chi-restraints excluded: chain A residue 3060 LEU Chi-restraints excluded: chain A residue 3149 VAL Chi-restraints excluded: chain A residue 3203 LEU Chi-restraints excluded: chain A residue 3204 ASP Chi-restraints excluded: chain A residue 3241 SER Chi-restraints excluded: chain A residue 3249 ILE Chi-restraints excluded: chain A residue 3284 HIS Chi-restraints excluded: chain A residue 3286 PHE Chi-restraints excluded: chain A residue 3333 ILE Chi-restraints excluded: chain A residue 3342 GLN Chi-restraints excluded: chain A residue 3366 ASN Chi-restraints excluded: chain A residue 3474 LEU Chi-restraints excluded: chain A residue 3502 LYS Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3625 ASP Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3693 THR Chi-restraints excluded: chain A residue 3702 ASN Chi-restraints excluded: chain A residue 3705 TYR Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3834 LEU Chi-restraints excluded: chain A residue 3857 PHE Chi-restraints excluded: chain A residue 3868 ILE Chi-restraints excluded: chain A residue 3889 ILE Chi-restraints excluded: chain A residue 3925 SER Chi-restraints excluded: chain A residue 3927 ILE Chi-restraints excluded: chain A residue 3934 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 143 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 0.0670 chunk 125 optimal weight: 2.9990 chunk 82 optimal weight: 0.0010 chunk 112 optimal weight: 0.5980 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2716 ASN ** A3340 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 = 0.3736 r_free = 0.3736 target = 0.147408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139414 restraints weight = 16816.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133429 restraints weight = 35510.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132445 restraints weight = 25717.806| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12393 Z= 0.108 Angle : 0.544 10.564 16794 Z= 0.282 Chirality : 0.039 0.177 1986 Planarity : 0.004 0.082 2083 Dihedral : 4.596 39.487 1676 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.21 % Favored : 94.59 % Rotamer: Outliers : 3.69 % Allowed : 14.76 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1517 helix: -0.28 (0.17), residues: 1017 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3354 HIS 0.002 0.000 HIS A3789 PHE 0.018 0.001 PHE A2398 TYR 0.011 0.001 TYR A2754 ARG 0.005 0.000 ARG A3636 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 466) hydrogen bonds : angle 3.48463 ( 1368) covalent geometry : bond 0.00242 (12393) covalent geometry : angle 0.54401 (16794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 2365 ILE cc_start: 0.1495 (OUTLIER) cc_final: 0.1251 (mp) REVERT: A 2466 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7984 (tp) REVERT: A 2520 ILE cc_start: 0.7015 (mt) cc_final: 0.6683 (tp) REVERT: A 2684 LEU cc_start: 0.7489 (mt) cc_final: 0.7183 (tt) REVERT: A 2921 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: A 2958 LYS cc_start: 0.7139 (tppt) cc_final: 0.6845 (mtmm) REVERT: A 2975 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.5100 (p90) REVERT: A 3205 ASP cc_start: 0.8244 (t0) cc_final: 0.7976 (t0) REVERT: A 3245 LYS cc_start: 0.6929 (mmmt) cc_final: 0.6132 (ptmt) REVERT: A 3410 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 3705 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7164 (t80) REVERT: A 3868 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 3892 GLU cc_start: 0.8024 (tp30) cc_final: 0.7757 (tp30) outliers start: 46 outliers final: 35 residues processed: 140 average time/residue: 0.2171 time to fit residues: 46.8947 Evaluate side-chains 140 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2381 LEU Chi-restraints excluded: chain A residue 2466 LEU Chi-restraints excluded: chain A residue 2583 VAL Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2686 SER Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2859 SER Chi-restraints excluded: chain A residue 2921 TYR Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 2975 TYR Chi-restraints excluded: chain A residue 3060 LEU Chi-restraints excluded: chain A residue 3149 VAL Chi-restraints excluded: chain A residue 3203 LEU Chi-restraints excluded: chain A residue 3204 ASP Chi-restraints excluded: chain A residue 3241 SER Chi-restraints excluded: chain A residue 3249 ILE Chi-restraints excluded: chain A residue 3284 HIS Chi-restraints excluded: chain A residue 3286 PHE Chi-restraints excluded: chain A residue 3321 LEU Chi-restraints excluded: chain A residue 3333 ILE Chi-restraints excluded: chain A residue 3366 ASN Chi-restraints excluded: chain A residue 3474 LEU Chi-restraints excluded: chain A residue 3502 LYS Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3625 ASP Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3693 THR Chi-restraints excluded: chain A residue 3702 ASN Chi-restraints excluded: chain A residue 3705 TYR Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3834 LEU Chi-restraints excluded: chain A residue 3857 PHE Chi-restraints excluded: chain A residue 3868 ILE Chi-restraints excluded: chain A residue 3889 ILE Chi-restraints excluded: chain A residue 3925 SER Chi-restraints excluded: chain A residue 3927 ILE Chi-restraints excluded: chain A residue 3934 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 83 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 139 optimal weight: 0.0020 chunk 90 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2378 ASN A2379 ASN A2716 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136906 restraints weight = 16839.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131771 restraints weight = 25073.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130036 restraints weight = 25578.964| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12393 Z= 0.164 Angle : 0.615 10.501 16794 Z= 0.313 Chirality : 0.042 0.184 1986 Planarity : 0.004 0.083 2083 Dihedral : 4.873 39.351 1676 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.33 % Favored : 93.47 % Rotamer: Outliers : 3.69 % Allowed : 15.16 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.22), residues: 1517 helix: -0.40 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -2.33 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A3354 HIS 0.003 0.001 HIS A3789 PHE 0.027 0.002 PHE A3623 TYR 0.012 0.001 TYR A2445 ARG 0.005 0.000 ARG A3636 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 466) hydrogen bonds : angle 3.80759 ( 1368) covalent geometry : bond 0.00386 (12393) covalent geometry : angle 0.61549 (16794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 98 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 2365 ILE cc_start: 0.1383 (OUTLIER) cc_final: 0.1095 (mp) REVERT: A 2466 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7949 (tp) REVERT: A 2520 ILE cc_start: 0.7112 (mt) cc_final: 0.6778 (tp) REVERT: A 2684 LEU cc_start: 0.7515 (mt) cc_final: 0.7246 (tt) REVERT: A 2921 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: A 2941 TRP cc_start: 0.6762 (t60) cc_final: 0.5898 (t-100) REVERT: A 2974 VAL cc_start: 0.8233 (m) cc_final: 0.7130 (p) REVERT: A 2975 TYR cc_start: 0.6691 (OUTLIER) cc_final: 0.5284 (p90) REVERT: A 3097 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7522 (mm-30) REVERT: A 3205 ASP cc_start: 0.8273 (t0) cc_final: 0.7992 (t0) REVERT: A 3245 LYS cc_start: 0.6866 (mmmt) cc_final: 0.6205 (ptmt) REVERT: A 3410 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7691 (tm-30) REVERT: A 3608 MET cc_start: 0.7722 (ttm) cc_final: 0.6151 (mmt) REVERT: A 3705 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.7084 (t80) REVERT: A 3892 GLU cc_start: 0.8090 (tp30) cc_final: 0.7834 (tp30) outliers start: 46 outliers final: 35 residues processed: 132 average time/residue: 0.2220 time to fit residues: 44.6732 Evaluate side-chains 136 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2365 ILE Chi-restraints excluded: chain A residue 2381 LEU Chi-restraints excluded: chain A residue 2403 THR Chi-restraints excluded: chain A residue 2466 LEU Chi-restraints excluded: chain A residue 2583 VAL Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2686 SER Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2859 SER Chi-restraints excluded: chain A residue 2921 TYR Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 2975 TYR Chi-restraints excluded: chain A residue 3060 LEU Chi-restraints excluded: chain A residue 3121 THR Chi-restraints excluded: chain A residue 3149 VAL Chi-restraints excluded: chain A residue 3203 LEU Chi-restraints excluded: chain A residue 3241 SER Chi-restraints excluded: chain A residue 3249 ILE Chi-restraints excluded: chain A residue 3284 HIS Chi-restraints excluded: chain A residue 3286 PHE Chi-restraints excluded: chain A residue 3321 LEU Chi-restraints excluded: chain A residue 3333 ILE Chi-restraints excluded: chain A residue 3474 LEU Chi-restraints excluded: chain A residue 3502 LYS Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3625 ASP Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3693 THR Chi-restraints excluded: chain A residue 3705 TYR Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3834 LEU Chi-restraints excluded: chain A residue 3857 PHE Chi-restraints excluded: chain A residue 3868 ILE Chi-restraints excluded: chain A residue 3889 ILE Chi-restraints excluded: chain A residue 3925 SER Chi-restraints excluded: chain A residue 3927 ILE Chi-restraints excluded: chain A residue 3934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 69 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 121 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2716 ASN ** A3340 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 = 0.3706 r_free = 0.3706 target = 0.144734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136836 restraints weight = 16651.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135733 restraints weight = 32137.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131011 restraints weight = 32380.355| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12393 Z= 0.127 Angle : 0.577 9.984 16794 Z= 0.295 Chirality : 0.040 0.181 1986 Planarity : 0.004 0.083 2083 Dihedral : 4.768 39.576 1676 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.54 % Favored : 94.26 % Rotamer: Outliers : 3.37 % Allowed : 15.32 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.22), residues: 1517 helix: -0.22 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -2.33 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A3354 HIS 0.003 0.001 HIS A3789 PHE 0.020 0.001 PHE A3623 TYR 0.012 0.001 TYR A2754 ARG 0.007 0.000 ARG A3636 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 466) hydrogen bonds : angle 3.65158 ( 1368) covalent geometry : bond 0.00294 (12393) covalent geometry : angle 0.57694 (16794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3034 Ramachandran restraints generated. 1517 Oldfield, 0 Emsley, 1517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 2466 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7981 (tp) REVERT: A 2520 ILE cc_start: 0.7147 (mt) cc_final: 0.6797 (tp) REVERT: A 2684 LEU cc_start: 0.7435 (mt) cc_final: 0.7168 (tt) REVERT: A 2921 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: A 2941 TRP cc_start: 0.6661 (t60) cc_final: 0.5808 (t-100) REVERT: A 2975 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.5255 (p90) REVERT: A 3097 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7386 (mm-30) REVERT: A 3205 ASP cc_start: 0.8279 (t0) cc_final: 0.7983 (t0) REVERT: A 3245 LYS cc_start: 0.6790 (mmmt) cc_final: 0.6059 (ptmt) REVERT: A 3410 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 3705 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7246 (t80) REVERT: A 3868 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 3892 GLU cc_start: 0.8045 (tp30) cc_final: 0.7793 (tp30) outliers start: 42 outliers final: 35 residues processed: 133 average time/residue: 0.2140 time to fit residues: 43.9568 Evaluate side-chains 138 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2381 LEU Chi-restraints excluded: chain A residue 2395 LEU Chi-restraints excluded: chain A residue 2466 LEU Chi-restraints excluded: chain A residue 2583 VAL Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2686 SER Chi-restraints excluded: chain A residue 2703 LEU Chi-restraints excluded: chain A residue 2775 THR Chi-restraints excluded: chain A residue 2859 SER Chi-restraints excluded: chain A residue 2921 TYR Chi-restraints excluded: chain A residue 2932 THR Chi-restraints excluded: chain A residue 2944 VAL Chi-restraints excluded: chain A residue 2975 TYR Chi-restraints excluded: chain A residue 3060 LEU Chi-restraints excluded: chain A residue 3149 VAL Chi-restraints excluded: chain A residue 3203 LEU Chi-restraints excluded: chain A residue 3241 SER Chi-restraints excluded: chain A residue 3249 ILE Chi-restraints excluded: chain A residue 3284 HIS Chi-restraints excluded: chain A residue 3286 PHE Chi-restraints excluded: chain A residue 3321 LEU Chi-restraints excluded: chain A residue 3333 ILE Chi-restraints excluded: chain A residue 3366 ASN Chi-restraints excluded: chain A residue 3474 LEU Chi-restraints excluded: chain A residue 3502 LYS Chi-restraints excluded: chain A residue 3518 VAL Chi-restraints excluded: chain A residue 3625 ASP Chi-restraints excluded: chain A residue 3664 LEU Chi-restraints excluded: chain A residue 3693 THR Chi-restraints excluded: chain A residue 3705 TYR Chi-restraints excluded: chain A residue 3745 LEU Chi-restraints excluded: chain A residue 3818 SER Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3834 LEU Chi-restraints excluded: chain A residue 3857 PHE Chi-restraints excluded: chain A residue 3868 ILE Chi-restraints excluded: chain A residue 3889 ILE Chi-restraints excluded: chain A residue 3925 SER Chi-restraints excluded: chain A residue 3927 ILE Chi-restraints excluded: chain A residue 3934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 chunk 127 optimal weight: 0.9990 chunk 138 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2369 HIS A2716 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137383 restraints weight = 16787.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131222 restraints weight = 27733.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129141 restraints weight = 22108.863| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12393 Z= 0.139 Angle : 0.591 9.993 16794 Z= 0.301 Chirality : 0.041 0.211 1986 Planarity : 0.004 0.083 2083 Dihedral : 4.798 39.141 1676 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.06 % Favored : 93.74 % Rotamer: Outliers : 3.21 % Allowed : 15.40 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 3.12 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1517 helix: -0.19 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A3354 HIS 0.003 0.001 HIS A3789 PHE 0.022 0.001 PHE A3623 TYR 0.012 0.001 TYR A2754 ARG 0.007 0.000 ARG A3636 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 466) hydrogen bonds : angle 3.69518 ( 1368) covalent geometry : bond 0.00328 (12393) covalent geometry : angle 0.59055 (16794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4055.17 seconds wall clock time: 71 minutes 40.85 seconds (4300.85 seconds total)