Starting phenix.real_space_refine (version: dev) on Mon Feb 20 12:48:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyd_0308/02_2023/6hyd_0308.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyd_0308/02_2023/6hyd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyd_0308/02_2023/6hyd_0308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyd_0308/02_2023/6hyd_0308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyd_0308/02_2023/6hyd_0308.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyd_0308/02_2023/6hyd_0308.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ARG 2609": "NH1" <-> "NH2" Residue "A ARG 3323": "NH1" <-> "NH2" Residue "A ARG 3964": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12168 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1574, 12168 Classifications: {'peptide': 1574} Incomplete info: {'truncation_to_alanine': 199} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 1540} Chain breaks: 16 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 610 Unresolved non-hydrogen angles: 772 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'UNK:plan-1': 31, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 21, 'PHE:plan': 3, 'GLU:plan': 37, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 355 Time building chain proxies: 7.30, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 2.0 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: 1.03 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: 4.23 Time building geometry restraints manager: 4.99 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: 99.76 - 106.95: 196 106.95 - 114.15: 7233 114.15 - 121.35: 6503 121.35 - 128.55: 2780 128.55 - 135.74: 82 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 2.440 nonbonded pdb=" OG SER A3952 " pdb=" OH TYR A4020 " model vdw 2.320 2.440 nonbonded pdb=" O ILE A2861 " pdb=" OG1 THR A2865 " model vdw 2.325 2.440 nonbonded pdb=" OG SER A3929 " pdb=" O LEU A3963 " model vdw 2.359 2.440 nonbonded pdb=" OD1 ASN A3947 " pdb=" OG SER A3950 " model vdw 2.370 2.440 ... (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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 12.040 Check model and map are aligned: 0.180 Process input model: 34.630 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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= 0.244 Angle : 0.851 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 % 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 325 time to evaluate : 1.460 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 327 average time/residue: 0.2733 time to fit residues: 124.8429 Evaluate side-chains 142 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2598 ASN A2676 ASN A2716 ASN A2844 HIS A3222 HIS A3262 ASN A3315 HIS ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3416 ASN A3462 GLN A3484 GLN A3618 GLN A3897 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 12393 Z= 0.301 Angle : 0.706 10.034 16794 Z= 0.367 Chirality : 0.043 0.166 1986 Planarity : 0.005 0.086 2083 Dihedral : 5.639 41.204 1676 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.13 % Favored : 93.67 % Rotamer Outliers : 3.53 % 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: -4.83 (0.16), residues: 1517 helix: -3.18 (0.11), residues: 1004 sheet: None (None), residues: 0 loop : -2.82 (0.24), residues: 513 *********************** 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 192 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 1.500 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 29 residues processed: 177 average time/residue: 0.2358 time to fit residues: 62.1347 Evaluate side-chains 156 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1456 time to fit residues: 9.2102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2611 HIS A2716 ASN A3011 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3618 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3625 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= 0.247 Angle : 0.637 11.973 16794 Z= 0.325 Chirality : 0.041 0.156 1986 Planarity : 0.004 0.086 2083 Dihedral : 5.363 39.814 1676 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.80 % Favored : 94.00 % Rotamer Outliers : 2.25 % 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: -3.70 (0.19), residues: 1517 helix: -2.19 (0.14), residues: 1020 sheet: None (None), residues: 0 loop : -2.69 (0.24), residues: 497 *********************** 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 154 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.378 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 147 average time/residue: 0.2242 time to fit residues: 50.2390 Evaluate side-chains 127 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1449 time to fit residues: 6.1803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2369 HIS ** A2419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2651 GLN A2716 ASN A3011 ASN ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3688 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12393 Z= 0.275 Angle : 0.640 9.632 16794 Z= 0.328 Chirality : 0.042 0.159 1986 Planarity : 0.004 0.086 2083 Dihedral : 5.380 39.790 1676 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.66 % Favored : 93.14 % Rotamer Outliers : 1.44 % 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: -3.18 (0.20), residues: 1517 helix: -1.75 (0.15), residues: 1022 sheet: None (None), residues: 0 loop : -2.59 (0.25), residues: 495 *********************** 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 129 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.596 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 124 average time/residue: 0.2388 time to fit residues: 45.7084 Evaluate side-chains 106 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1189 time to fit residues: 3.8232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 chunk 104 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12393 Z= 0.203 Angle : 0.580 9.512 16794 Z= 0.299 Chirality : 0.040 0.154 1986 Planarity : 0.004 0.085 2083 Dihedral : 5.113 39.898 1676 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.67 % Favored : 94.13 % Rotamer Outliers : 1.52 % 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: -2.68 (0.21), residues: 1517 helix: -1.34 (0.16), residues: 1021 sheet: None (None), residues: 0 loop : -2.46 (0.26), residues: 496 *********************** 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 126 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.561 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 120 average time/residue: 0.2407 time to fit residues: 44.5008 Evaluate side-chains 108 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1254 time to fit residues: 4.4082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 12393 Z= 0.239 Angle : 0.605 9.381 16794 Z= 0.308 Chirality : 0.041 0.157 1986 Planarity : 0.004 0.085 2083 Dihedral : 5.130 39.690 1676 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.53 % Favored : 93.28 % Rotamer Outliers : 1.12 % 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: -2.45 (0.21), residues: 1517 helix: -1.16 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -2.38 (0.26), residues: 492 *********************** 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 122 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.371 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 121 average time/residue: 0.2419 time to fit residues: 44.6476 Evaluate side-chains 103 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1253 time to fit residues: 2.9083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 127 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 94 optimal weight: 0.0370 chunk 92 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 93 optimal weight: 0.5980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4472 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= 0.182 Angle : 0.574 9.218 16794 Z= 0.293 Chirality : 0.039 0.155 1986 Planarity : 0.004 0.085 2083 Dihedral : 4.891 39.743 1676 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.87 % Favored : 93.94 % Rotamer Outliers : 1.36 % 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: -2.04 (0.21), residues: 1517 helix: -0.83 (0.17), residues: 1023 sheet: None (None), residues: 0 loop : -2.26 (0.26), residues: 494 *********************** 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 119 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.483 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 115 average time/residue: 0.2593 time to fit residues: 46.4604 Evaluate side-chains 101 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1284 time to fit residues: 3.5687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 118 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12393 Z= 0.217 Angle : 0.602 10.083 16794 Z= 0.304 Chirality : 0.041 0.157 1986 Planarity : 0.004 0.085 2083 Dihedral : 4.952 39.638 1676 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.26 % Favored : 93.54 % Rotamer Outliers : 0.72 % 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: -1.88 (0.21), residues: 1517 helix: -0.70 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -2.22 (0.26), residues: 497 *********************** 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 109 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.481 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 106 average time/residue: 0.2496 time to fit residues: 40.4553 Evaluate side-chains 101 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1156 time to fit residues: 3.1542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 127 optimal weight: 0.2980 chunk 133 optimal weight: 0.0270 chunk 140 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12393 Z= 0.192 Angle : 0.591 11.792 16794 Z= 0.297 Chirality : 0.040 0.156 1986 Planarity : 0.004 0.085 2083 Dihedral : 4.851 39.631 1676 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.87 % Favored : 93.94 % Rotamer Outliers : 0.48 % 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: -1.58 (0.22), residues: 1517 helix: -0.45 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 503 *********************** 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 109 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.446 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 106 average time/residue: 0.2519 time to fit residues: 40.8402 Evaluate side-chains 101 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1176 time to fit residues: 2.9942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 103 optimal weight: 0.2980 chunk 156 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3688 GLN A3697 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12393 Z= 0.222 Angle : 0.614 11.782 16794 Z= 0.308 Chirality : 0.041 0.156 1986 Planarity : 0.004 0.085 2083 Dihedral : 4.935 39.597 1676 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.06 % Favored : 93.74 % Rotamer Outliers : 0.24 % 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: -1.54 (0.22), residues: 1517 helix: -0.43 (0.17), residues: 1015 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 502 ********************** 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 102 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.432 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 0.2388 time to fit residues: 36.6284 Evaluate side-chains 97 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.622 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1196 time to fit residues: 2.3225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 109 optimal weight: 0.0170 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3697 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128213 restraints weight = 16448.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128563 restraints weight = 14005.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128821 restraints weight = 12226.742| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 12393 Z= 0.151 Angle : 0.561 13.486 16794 Z= 0.283 Chirality : 0.038 0.158 1986 Planarity : 0.004 0.085 2083 Dihedral : 4.603 39.293 1676 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.21 % Favored : 94.59 % Rotamer Outliers : 0.48 % 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: -1.15 (0.22), residues: 1517 helix: -0.07 (0.17), residues: 1019 sheet: None (None), residues: 0 loop : -2.11 (0.26), residues: 498 =============================================================================== Job complete usr+sys time: 2234.88 seconds wall clock time: 42 minutes 8.16 seconds (2528.16 seconds total)