Starting phenix.real_space_refine on Thu May 22 22:46:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmm_44703/05_2025/9bmm_44703.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmm_44703/05_2025/9bmm_44703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmm_44703/05_2025/9bmm_44703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmm_44703/05_2025/9bmm_44703.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmm_44703/05_2025/9bmm_44703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmm_44703/05_2025/9bmm_44703.cif" } resolution = 3.1 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= -0.001 sd= 0.065 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 14635 2.51 5 N 3980 2.21 5 O 4300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23038 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2859, 22925 Classifications: {'peptide': 2859} Link IDs: {'PTRANS': 130, 'TRANS': 2728} Chain breaks: 3 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 12.53, per 1000 atoms: 0.54 Number of scatterers: 23038 At special positions: 0 Unit cell: (145.824, 186.186, 149.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 113 16.00 P 9 15.00 Mg 1 11.99 O 4300 8.00 N 3980 7.00 C 14635 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: 5.45 Conformation dependent library (CDL) restraints added in 2.8 seconds 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 18 sheets defined 63.3% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 1536 through 1554 Processing helix chain 'A' and resid 1556 through 1560 Processing helix chain 'A' and resid 1561 through 1583 Processing helix chain 'A' and resid 1587 through 1593 removed outlier: 3.695A pdb=" N ASN A1593 " --> pdb=" O MET A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1625 removed outlier: 3.508A pdb=" N SER A1600 " --> pdb=" O GLY A1596 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A1625 " --> pdb=" O ARG A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1648 through 1657 removed outlier: 4.084A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE A1654 " --> pdb=" O GLN A1651 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS A1655 " --> pdb=" O LYS A1652 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A1657 " --> pdb=" O PHE A1654 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.532A pdb=" N GLU A1706 " --> pdb=" O LEU A1702 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1769 removed outlier: 3.830A pdb=" N VAL A1751 " --> pdb=" O ALA A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1772 No H-bonds generated for 'chain 'A' and resid 1770 through 1772' Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.541A pdb=" N VAL A1781 " --> pdb=" O PRO A1777 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1828 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.881A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A1987 " --> pdb=" O ARG A1983 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2145 Processing helix chain 'A' and resid 2146 through 2149 Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 removed outlier: 3.893A pdb=" N GLU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2255 through 2259 removed outlier: 3.835A pdb=" N ILE A2259 " --> pdb=" O PRO A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2311 through 2314 removed outlier: 3.572A pdb=" N ASN A2314 " --> pdb=" O TRP A2311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2311 through 2314' Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.921A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2441 Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.737A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.552A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2610 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.126A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 3.507A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2757 through 2764 Proline residue: A2760 - end of helix removed outlier: 4.766A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.826A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2927 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.879A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.861A pdb=" N ALA A3027 " --> pdb=" O GLY A3023 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3062 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.641A pdb=" N LYS A3076 " --> pdb=" O SER A3072 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 removed outlier: 3.597A pdb=" N ASN A3087 " --> pdb=" O PRO A3083 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3111 through 3113 No H-bonds generated for 'chain 'A' and resid 3111 through 3113' Processing helix chain 'A' and resid 3138 through 3164 removed outlier: 3.506A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3241 removed outlier: 3.772A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3495 removed outlier: 4.663A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3517 removed outlier: 4.699A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3580 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.808A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 3.804A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A3696 " --> pdb=" O LEU A3692 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3756 Processing helix chain 'A' and resid 3763 through 3818 removed outlier: 4.249A pdb=" N GLN A3800 " --> pdb=" O THR A3796 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.514A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 3.552A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3876 through 3894 removed outlier: 4.524A pdb=" N ILE A3881 " --> pdb=" O HIS A3877 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR A3882 " --> pdb=" O GLN A3878 " (cutoff:3.500A) Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3940 removed outlier: 3.589A pdb=" N CYS A3940 " --> pdb=" O VAL A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.745A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.185A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4019 through 4023 Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.666A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.642A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.099A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.669A pdb=" N MET A4107 " --> pdb=" O PRO A4103 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.530A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4193 Processing helix chain 'A' and resid 4196 through 4201 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.524A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4324 through 4327 Processing helix chain 'A' and resid 4328 through 4346 removed outlier: 3.509A pdb=" N MET A4346 " --> pdb=" O LYS A4342 " (cutoff:3.500A) Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.339A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4502 through 4506 Processing helix chain 'A' and resid 4512 through 4514 No H-bonds generated for 'chain 'A' and resid 4512 through 4514' Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.706A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A4521 " --> pdb=" O PRO A4517 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A4522 " --> pdb=" O GLU A4518 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 3.505A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1931 Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2000 Processing sheet with id=AA6, first strand: chain 'A' and resid 2249 through 2254 Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 5.931A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 6.855A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.291A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 6.196A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.156A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A4128 " --> pdb=" O MET A4043 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4283 through 4289 removed outlier: 7.466A pdb=" N LYS A4287 " --> pdb=" O ILE A4294 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A4294 " --> pdb=" O LYS A4287 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A4289 " --> pdb=" O LYS A4292 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.292A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.254A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1364 hydrogen bonds defined for protein. 3960 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: 12.51 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5809 1.33 - 1.45: 4381 1.45 - 1.57: 13136 1.57 - 1.70: 14 1.70 - 1.82: 189 Bond restraints: 23529 Sorted by residual: bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" N ILE A1692 " pdb=" CA ILE A1692 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.08e-02 8.57e+03 1.08e+01 bond pdb=" N VAL A1690 " pdb=" CA VAL A1690 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.24e+00 bond pdb=" N THR A2017 " pdb=" CA THR A2017 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.27e-02 6.20e+03 7.47e+00 ... (remaining 23524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 31508 2.23 - 4.47: 358 4.47 - 6.70: 36 6.70 - 8.93: 9 8.93 - 11.16: 4 Bond angle restraints: 31915 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 131.96 7.91 1.00e+00 1.00e+00 6.26e+01 angle pdb=" PA ATP A4702 " pdb=" O3A ATP A4702 " pdb=" PB ATP A4702 " ideal model delta sigma weight residual 136.83 130.93 5.90 1.00e+00 1.00e+00 3.48e+01 angle pdb=" N ILE A1692 " pdb=" CA ILE A1692 " pdb=" C ILE A1692 " ideal model delta sigma weight residual 113.42 108.01 5.41 1.17e+00 7.31e-01 2.14e+01 angle pdb=" C5' ATP A4702 " pdb=" O5' ATP A4702 " pdb=" PA ATP A4702 " ideal model delta sigma weight residual 121.27 117.42 3.85 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA THR A2017 " pdb=" C THR A2017 " pdb=" O THR A2017 " ideal model delta sigma weight residual 121.56 117.49 4.07 1.09e+00 8.42e-01 1.40e+01 ... (remaining 31910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 13159 23.81 - 47.61: 946 47.61 - 71.42: 146 71.42 - 95.22: 29 95.22 - 119.03: 2 Dihedral angle restraints: 14282 sinusoidal: 5915 harmonic: 8367 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 -179.03 119.03 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 -167.04 107.04 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual -60.00 -138.34 78.34 1 2.00e+01 2.50e-03 1.91e+01 ... (remaining 14279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2756 0.041 - 0.081: 601 0.081 - 0.121: 210 0.121 - 0.162: 20 0.162 - 0.202: 8 Chirality restraints: 3595 Sorted by residual: chirality pdb=" CA VAL A1880 " pdb=" N VAL A1880 " pdb=" C VAL A1880 " pdb=" CB VAL A1880 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE A1692 " pdb=" N ILE A1692 " pdb=" C ILE A1692 " pdb=" CB ILE A1692 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CA ILE A1997 " pdb=" N ILE A1997 " pdb=" C ILE A1997 " pdb=" CB ILE A1997 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 3592 not shown) Planarity restraints: 4090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A4376 " 0.013 2.00e-02 2.50e+03 1.41e-02 4.98e+00 pdb=" CG TRP A4376 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A4376 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A4376 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A4376 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A4376 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A4376 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4376 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4376 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A4376 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A3136 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO A3137 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A3137 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A3137 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A2318 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C VAL A2318 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL A2318 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A2319 " -0.010 2.00e-02 2.50e+03 ... (remaining 4087 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 105 2.52 - 3.11: 16701 3.11 - 3.71: 36311 3.71 - 4.30: 51150 4.30 - 4.90: 87002 Nonbonded interactions: 191269 Sorted by model distance: nonbonded pdb=" OG SER A2231 " pdb="MG MG A4705 " model vdw 1.921 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4705 " model vdw 2.007 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4705 " model vdw 2.044 2.170 nonbonded pdb=" NE2 GLN A2834 " pdb=" OD2 ASP A2847 " model vdw 2.206 3.120 nonbonded pdb=" O ILE A1550 " pdb=" OG SER A1554 " model vdw 2.229 3.040 ... (remaining 191264 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 54.070 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.003 0.109 23529 Z= 0.182 Angle : 0.543 11.164 31915 Z= 0.312 Chirality : 0.039 0.202 3595 Planarity : 0.004 0.054 4090 Dihedral : 16.213 119.029 8848 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.24 % Allowed : 11.89 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2851 helix: 1.54 (0.12), residues: 1645 sheet: -0.51 (0.33), residues: 246 loop : 0.65 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A4376 HIS 0.003 0.000 HIS A4006 PHE 0.010 0.001 PHE A4413 TYR 0.013 0.001 TYR A2641 ARG 0.010 0.000 ARG A4195 Details of bonding type rmsd hydrogen bonds : bond 0.20041 ( 1364) hydrogen bonds : angle 6.51084 ( 3960) covalent geometry : bond 0.00300 (23529) covalent geometry : angle 0.54305 (31915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 226 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1700 GLU cc_start: 0.7209 (tp30) cc_final: 0.6961 (tp30) REVERT: A 3972 TYR cc_start: 0.7900 (t80) cc_final: 0.7677 (t80) outliers start: 6 outliers final: 3 residues processed: 231 average time/residue: 0.3740 time to fit residues: 132.8560 Evaluate side-chains 200 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1991 ASP Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 4127 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 223 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.138587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106411 restraints weight = 31725.075| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.23 r_work: 0.3142 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23529 Z= 0.131 Angle : 0.503 6.829 31915 Z= 0.258 Chirality : 0.039 0.139 3595 Planarity : 0.004 0.050 4090 Dihedral : 6.110 102.269 3180 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.46 % Allowed : 11.14 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.16), residues: 2851 helix: 2.18 (0.13), residues: 1655 sheet: -0.42 (0.33), residues: 242 loop : 0.84 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4376 HIS 0.004 0.001 HIS A4006 PHE 0.015 0.001 PHE A3004 TYR 0.019 0.001 TYR A1546 ARG 0.010 0.000 ARG A2869 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 1364) hydrogen bonds : angle 4.41573 ( 3960) covalent geometry : bond 0.00277 (23529) covalent geometry : angle 0.50341 (31915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2189 MET cc_start: 0.8684 (mtt) cc_final: 0.8386 (mtm) REVERT: A 2763 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7562 (mmm160) REVERT: A 3006 GLU cc_start: 0.7756 (tp30) cc_final: 0.7475 (tp30) REVERT: A 3523 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7895 (mm-40) REVERT: A 3624 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8245 (mt-10) REVERT: A 3793 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: A 3905 PHE cc_start: 0.8738 (m-80) cc_final: 0.8512 (m-80) REVERT: A 3913 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: A 4292 LYS cc_start: 0.8164 (tttm) cc_final: 0.7858 (ttpt) outliers start: 37 outliers final: 20 residues processed: 250 average time/residue: 0.3945 time to fit residues: 154.0981 Evaluate side-chains 217 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2118 ARG Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3793 GLU Chi-restraints excluded: chain A residue 3913 GLU Chi-restraints excluded: chain A residue 3948 ILE Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4405 ILE Chi-restraints excluded: chain A residue 4533 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 184 optimal weight: 6.9990 chunk 101 optimal weight: 0.0870 chunk 266 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 283 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1784 ASN A3047 HIS A4062 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105024 restraints weight = 31349.345| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.12 r_work: 0.3159 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23529 Z= 0.111 Angle : 0.468 6.869 31915 Z= 0.234 Chirality : 0.038 0.151 3595 Planarity : 0.004 0.051 4090 Dihedral : 5.929 94.715 3177 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.26 % Allowed : 11.97 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.16), residues: 2851 helix: 2.37 (0.13), residues: 1647 sheet: -0.38 (0.34), residues: 233 loop : 0.87 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.005 0.001 HIS A4006 PHE 0.013 0.001 PHE A2682 TYR 0.022 0.001 TYR A1546 ARG 0.006 0.000 ARG A2869 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 1364) hydrogen bonds : angle 4.05345 ( 3960) covalent geometry : bond 0.00240 (23529) covalent geometry : angle 0.46779 (31915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1682 GLU cc_start: 0.8384 (tt0) cc_final: 0.8053 (tt0) REVERT: A 1694 GLU cc_start: 0.7226 (pm20) cc_final: 0.6397 (pm20) REVERT: A 1695 HIS cc_start: 0.7681 (m90) cc_final: 0.6986 (m90) REVERT: A 1814 GLU cc_start: 0.7513 (tp30) cc_final: 0.6558 (tp30) REVERT: A 1943 ARG cc_start: 0.8337 (mpt180) cc_final: 0.7991 (mpt-90) REVERT: A 2536 ASP cc_start: 0.8058 (m-30) cc_final: 0.7758 (t0) REVERT: A 2763 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7600 (mmm160) REVERT: A 3006 GLU cc_start: 0.7746 (tp30) cc_final: 0.7498 (tp30) REVERT: A 3043 MET cc_start: 0.7713 (pmm) cc_final: 0.7480 (pmm) REVERT: A 3104 GLN cc_start: 0.8726 (mt0) cc_final: 0.8524 (mt0) REVERT: A 3199 MET cc_start: 0.8113 (tmm) cc_final: 0.7663 (tmm) REVERT: A 3905 PHE cc_start: 0.8807 (m-80) cc_final: 0.8593 (m-80) REVERT: A 4292 LYS cc_start: 0.8174 (tttm) cc_final: 0.7951 (ttpt) outliers start: 32 outliers final: 19 residues processed: 251 average time/residue: 0.3874 time to fit residues: 151.5124 Evaluate side-chains 222 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2997 SER Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4405 ILE Chi-restraints excluded: chain A residue 4533 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 227 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 231 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 260 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 192 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN A2827 HIS A3499 GLN A3535 HIS A4062 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105537 restraints weight = 31723.860| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.22 r_work: 0.3164 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23529 Z= 0.102 Angle : 0.459 6.949 31915 Z= 0.228 Chirality : 0.038 0.166 3595 Planarity : 0.004 0.052 4090 Dihedral : 5.635 87.674 3175 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.42 % Allowed : 12.60 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.16), residues: 2851 helix: 2.46 (0.13), residues: 1650 sheet: -0.35 (0.33), residues: 233 loop : 0.93 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1701 HIS 0.005 0.001 HIS A4006 PHE 0.012 0.001 PHE A2912 TYR 0.023 0.001 TYR A1546 ARG 0.005 0.000 ARG A3160 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 1364) hydrogen bonds : angle 3.87810 ( 3960) covalent geometry : bond 0.00222 (23529) covalent geometry : angle 0.45862 (31915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 2.377 Fit side-chains revert: symmetry clash REVERT: A 1682 GLU cc_start: 0.8417 (tt0) cc_final: 0.8050 (tt0) REVERT: A 1695 HIS cc_start: 0.7662 (m90) cc_final: 0.6780 (m90) REVERT: A 1943 ARG cc_start: 0.8271 (mpt180) cc_final: 0.7829 (mpt-90) REVERT: A 2320 ASP cc_start: 0.8471 (m-30) cc_final: 0.8121 (m-30) REVERT: A 2536 ASP cc_start: 0.7952 (m-30) cc_final: 0.7622 (t0) REVERT: A 2763 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7560 (mmm160) REVERT: A 3006 GLU cc_start: 0.7661 (tp30) cc_final: 0.7326 (tp30) REVERT: A 3169 MET cc_start: 0.8585 (mmp) cc_final: 0.8233 (mmp) REVERT: A 3196 GLU cc_start: 0.7866 (tt0) cc_final: 0.7259 (tp30) REVERT: A 3199 MET cc_start: 0.8018 (tmm) cc_final: 0.7555 (tmm) REVERT: A 3464 ASP cc_start: 0.4441 (OUTLIER) cc_final: 0.4061 (p0) REVERT: A 3695 ARG cc_start: 0.8931 (mtt-85) cc_final: 0.8186 (mtt-85) REVERT: A 3793 GLU cc_start: 0.7976 (tt0) cc_final: 0.7669 (pt0) REVERT: A 3795 GLU cc_start: 0.7413 (tp30) cc_final: 0.6933 (tm-30) REVERT: A 3799 GLN cc_start: 0.8661 (mt0) cc_final: 0.8180 (mm-40) REVERT: A 3913 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: A 4270 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8344 (mt-10) REVERT: A 4292 LYS cc_start: 0.8132 (tttm) cc_final: 0.7861 (ttpt) outliers start: 36 outliers final: 22 residues processed: 259 average time/residue: 0.3761 time to fit residues: 151.2104 Evaluate side-chains 235 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2997 SER Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3464 ASP Chi-restraints excluded: chain A residue 3913 GLU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4405 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 42 optimal weight: 0.8980 chunk 152 optimal weight: 0.2980 chunk 254 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 274 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4012 ASN A4062 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107631 restraints weight = 31846.292| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.17 r_work: 0.3164 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23529 Z= 0.106 Angle : 0.457 6.926 31915 Z= 0.227 Chirality : 0.038 0.142 3595 Planarity : 0.003 0.053 4090 Dihedral : 5.473 80.480 3175 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.38 % Allowed : 13.47 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.16), residues: 2851 helix: 2.56 (0.13), residues: 1650 sheet: -0.36 (0.33), residues: 233 loop : 0.92 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2234 HIS 0.004 0.001 HIS A4006 PHE 0.012 0.001 PHE A2912 TYR 0.023 0.001 TYR A1546 ARG 0.006 0.000 ARG A3160 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1364) hydrogen bonds : angle 3.79007 ( 3960) covalent geometry : bond 0.00234 (23529) covalent geometry : angle 0.45747 (31915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 2.461 Fit side-chains revert: symmetry clash REVERT: A 1682 GLU cc_start: 0.8432 (tt0) cc_final: 0.8108 (tt0) REVERT: A 1943 ARG cc_start: 0.8307 (mpt180) cc_final: 0.7913 (mpt-90) REVERT: A 2215 GLN cc_start: 0.8383 (mm110) cc_final: 0.8161 (tt0) REVERT: A 2312 VAL cc_start: 0.9392 (OUTLIER) cc_final: 0.9122 (p) REVERT: A 2320 ASP cc_start: 0.8535 (m-30) cc_final: 0.8329 (m-30) REVERT: A 2763 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7670 (mmm160) REVERT: A 3006 GLU cc_start: 0.7738 (tp30) cc_final: 0.7405 (tp30) REVERT: A 3169 MET cc_start: 0.8538 (mmp) cc_final: 0.8221 (mmp) REVERT: A 3196 GLU cc_start: 0.7961 (tt0) cc_final: 0.7403 (tp30) REVERT: A 3199 MET cc_start: 0.8057 (tmm) cc_final: 0.7569 (tmm) REVERT: A 3464 ASP cc_start: 0.4518 (OUTLIER) cc_final: 0.4118 (p0) REVERT: A 3795 GLU cc_start: 0.7484 (tp30) cc_final: 0.7057 (tm-30) REVERT: A 3799 GLN cc_start: 0.8706 (mt0) cc_final: 0.8259 (mm-40) REVERT: A 3913 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: A 4110 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8721 (tp30) REVERT: A 4231 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7688 (mm-40) REVERT: A 4292 LYS cc_start: 0.8250 (tttm) cc_final: 0.7931 (tttt) REVERT: A 4426 ASP cc_start: 0.7997 (t0) cc_final: 0.7776 (t0) REVERT: A 4547 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7504 (p) outliers start: 35 outliers final: 21 residues processed: 255 average time/residue: 0.3813 time to fit residues: 150.7818 Evaluate side-chains 234 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2997 SER Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3464 ASP Chi-restraints excluded: chain A residue 3913 GLU Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4110 GLU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4231 GLN Chi-restraints excluded: chain A residue 4405 ILE Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4547 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 201 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2827 HIS ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3744 GLN A4062 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106695 restraints weight = 31610.502| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.22 r_work: 0.3158 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23529 Z= 0.116 Angle : 0.470 6.832 31915 Z= 0.234 Chirality : 0.038 0.147 3595 Planarity : 0.004 0.053 4090 Dihedral : 5.399 78.768 3175 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.66 % Allowed : 13.78 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.60 (0.16), residues: 2851 helix: 2.57 (0.13), residues: 1651 sheet: -0.41 (0.33), residues: 233 loop : 0.90 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1701 HIS 0.003 0.001 HIS A4006 PHE 0.013 0.001 PHE A2912 TYR 0.022 0.001 TYR A1546 ARG 0.006 0.000 ARG A3654 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1364) hydrogen bonds : angle 3.76393 ( 3960) covalent geometry : bond 0.00266 (23529) covalent geometry : angle 0.46991 (31915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 2.744 Fit side-chains revert: symmetry clash REVERT: A 1682 GLU cc_start: 0.8430 (tt0) cc_final: 0.8064 (tt0) REVERT: A 1943 ARG cc_start: 0.8270 (mpt180) cc_final: 0.7844 (mpt-90) REVERT: A 2215 GLN cc_start: 0.8324 (mm110) cc_final: 0.8053 (tt0) REVERT: A 2312 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9066 (p) REVERT: A 2763 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7646 (mmm160) REVERT: A 3006 GLU cc_start: 0.7724 (tp30) cc_final: 0.7320 (tp30) REVERT: A 3169 MET cc_start: 0.8550 (mmp) cc_final: 0.8248 (mmp) REVERT: A 3196 GLU cc_start: 0.7920 (tt0) cc_final: 0.7307 (tp30) REVERT: A 3199 MET cc_start: 0.8025 (tmm) cc_final: 0.7504 (tmm) REVERT: A 3464 ASP cc_start: 0.4671 (OUTLIER) cc_final: 0.4314 (p0) REVERT: A 3695 ARG cc_start: 0.8912 (mtt-85) cc_final: 0.8076 (mtt-85) REVERT: A 3795 GLU cc_start: 0.7414 (tp30) cc_final: 0.6930 (tm-30) REVERT: A 3799 GLN cc_start: 0.8663 (mt0) cc_final: 0.8126 (mm-40) REVERT: A 3913 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: A 4110 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8739 (tp30) REVERT: A 4231 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7601 (mm-40) REVERT: A 4292 LYS cc_start: 0.8211 (tttm) cc_final: 0.7861 (tttt) REVERT: A 4426 ASP cc_start: 0.7878 (t0) cc_final: 0.7654 (t0) REVERT: A 4547 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7432 (p) outliers start: 42 outliers final: 28 residues processed: 255 average time/residue: 0.3697 time to fit residues: 147.6022 Evaluate side-chains 243 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2997 SER Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3464 ASP Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3913 GLU Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4110 GLU Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4231 GLN Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4405 ILE Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4547 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 189 optimal weight: 0.0770 chunk 264 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 79 optimal weight: 0.0570 chunk 143 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 210 optimal weight: 0.0980 chunk 218 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2005 GLN A2827 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107988 restraints weight = 31742.676| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.18 r_work: 0.3176 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23529 Z= 0.099 Angle : 0.459 7.964 31915 Z= 0.227 Chirality : 0.038 0.146 3595 Planarity : 0.003 0.052 4090 Dihedral : 5.301 75.428 3175 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.38 % Allowed : 14.02 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.16), residues: 2851 helix: 2.65 (0.13), residues: 1651 sheet: -0.36 (0.33), residues: 233 loop : 0.91 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.003 0.000 HIS A4006 PHE 0.011 0.001 PHE A2912 TYR 0.023 0.001 TYR A1546 ARG 0.005 0.000 ARG A3160 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1364) hydrogen bonds : angle 3.68763 ( 3960) covalent geometry : bond 0.00217 (23529) covalent geometry : angle 0.45860 (31915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1682 GLU cc_start: 0.8403 (tt0) cc_final: 0.8070 (tt0) REVERT: A 1943 ARG cc_start: 0.8277 (mpt180) cc_final: 0.7861 (mpt-90) REVERT: A 2215 GLN cc_start: 0.8335 (mm110) cc_final: 0.7993 (mt0) REVERT: A 2312 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9123 (p) REVERT: A 2763 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7793 (mmm160) REVERT: A 2869 ARG cc_start: 0.7248 (tpp-160) cc_final: 0.6308 (tpp-160) REVERT: A 3006 GLU cc_start: 0.7748 (tp30) cc_final: 0.7387 (tp30) REVERT: A 3043 MET cc_start: 0.7858 (pmm) cc_final: 0.7607 (pmm) REVERT: A 3169 MET cc_start: 0.8567 (mmp) cc_final: 0.8292 (mmp) REVERT: A 3196 GLU cc_start: 0.7940 (tt0) cc_final: 0.7380 (tp30) REVERT: A 3199 MET cc_start: 0.8083 (tmm) cc_final: 0.7785 (tmm) REVERT: A 3464 ASP cc_start: 0.4727 (OUTLIER) cc_final: 0.4351 (p0) REVERT: A 3795 GLU cc_start: 0.7506 (tp30) cc_final: 0.7291 (tm-30) REVERT: A 3913 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: A 4110 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8775 (tp30) REVERT: A 4231 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7644 (mm-40) REVERT: A 4292 LYS cc_start: 0.8242 (tttm) cc_final: 0.7911 (tttt) REVERT: A 4344 LEU cc_start: 0.9063 (tp) cc_final: 0.8843 (tp) REVERT: A 4377 MET cc_start: 0.7989 (ttm) cc_final: 0.7761 (mtp) REVERT: A 4426 ASP cc_start: 0.7935 (t0) cc_final: 0.7727 (t0) REVERT: A 4547 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7527 (p) outliers start: 35 outliers final: 21 residues processed: 264 average time/residue: 0.3764 time to fit residues: 155.2684 Evaluate side-chains 241 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2997 SER Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3464 ASP Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3913 GLU Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4110 GLU Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4231 GLN Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4405 ILE Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4547 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 27 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 250 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2827 HIS ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3744 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108027 restraints weight = 31790.459| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.19 r_work: 0.3179 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23529 Z= 0.101 Angle : 0.468 9.265 31915 Z= 0.230 Chirality : 0.038 0.171 3595 Planarity : 0.003 0.052 4090 Dihedral : 5.262 72.962 3175 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.46 % Allowed : 14.18 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.16), residues: 2851 helix: 2.70 (0.13), residues: 1649 sheet: -0.42 (0.33), residues: 240 loop : 0.93 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A4376 HIS 0.003 0.000 HIS A4006 PHE 0.012 0.001 PHE A2912 TYR 0.023 0.001 TYR A1546 ARG 0.006 0.000 ARG A3160 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 1364) hydrogen bonds : angle 3.65910 ( 3960) covalent geometry : bond 0.00225 (23529) covalent geometry : angle 0.46776 (31915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1682 GLU cc_start: 0.8403 (tt0) cc_final: 0.8062 (tt0) REVERT: A 1694 GLU cc_start: 0.7318 (pm20) cc_final: 0.6792 (pm20) REVERT: A 1943 ARG cc_start: 0.8255 (mpt180) cc_final: 0.7845 (mpt-90) REVERT: A 2215 GLN cc_start: 0.8342 (mm110) cc_final: 0.8003 (mt0) REVERT: A 2312 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9123 (p) REVERT: A 2763 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7791 (mmm160) REVERT: A 2869 ARG cc_start: 0.7258 (tpp-160) cc_final: 0.6497 (tpp-160) REVERT: A 3006 GLU cc_start: 0.7751 (tp30) cc_final: 0.7377 (tp30) REVERT: A 3043 MET cc_start: 0.7900 (pmm) cc_final: 0.7624 (pmm) REVERT: A 3169 MET cc_start: 0.8564 (mmp) cc_final: 0.8316 (mmp) REVERT: A 3196 GLU cc_start: 0.7894 (tt0) cc_final: 0.7299 (tp30) REVERT: A 3199 MET cc_start: 0.8082 (tmm) cc_final: 0.7785 (tmm) REVERT: A 3464 ASP cc_start: 0.4710 (OUTLIER) cc_final: 0.4279 (p0) REVERT: A 3695 ARG cc_start: 0.8941 (mtt-85) cc_final: 0.8206 (mtt-85) REVERT: A 3795 GLU cc_start: 0.7573 (tp30) cc_final: 0.7354 (tm-30) REVERT: A 3913 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: A 4231 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7655 (mm-40) REVERT: A 4292 LYS cc_start: 0.8240 (tttm) cc_final: 0.7910 (tttt) REVERT: A 4344 LEU cc_start: 0.9061 (tp) cc_final: 0.8840 (tp) REVERT: A 4377 MET cc_start: 0.8045 (ttm) cc_final: 0.7792 (mtp) REVERT: A 4426 ASP cc_start: 0.7947 (t0) cc_final: 0.7732 (t0) REVERT: A 4547 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7547 (p) outliers start: 37 outliers final: 29 residues processed: 252 average time/residue: 0.3725 time to fit residues: 146.4433 Evaluate side-chains 247 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2997 SER Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3464 ASP Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3774 LYS Chi-restraints excluded: chain A residue 3913 GLU Chi-restraints excluded: chain A residue 3927 LEU Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4231 GLN Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4405 ILE Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4547 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 184 optimal weight: 0.2980 chunk 202 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 273 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103489 restraints weight = 31593.325| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.21 r_work: 0.3137 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23529 Z= 0.144 Angle : 0.492 7.518 31915 Z= 0.242 Chirality : 0.039 0.163 3595 Planarity : 0.004 0.054 4090 Dihedral : 5.301 83.627 3175 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.66 % Allowed : 14.14 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.16), residues: 2851 helix: 2.65 (0.13), residues: 1645 sheet: -0.46 (0.33), residues: 234 loop : 0.86 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1701 HIS 0.003 0.001 HIS A4006 PHE 0.014 0.001 PHE A2912 TYR 0.022 0.001 TYR A1546 ARG 0.005 0.000 ARG A3160 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 1364) hydrogen bonds : angle 3.72795 ( 3960) covalent geometry : bond 0.00339 (23529) covalent geometry : angle 0.49236 (31915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 2.490 Fit side-chains revert: symmetry clash REVERT: A 1682 GLU cc_start: 0.8408 (tt0) cc_final: 0.8123 (tt0) REVERT: A 1808 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8031 (mt) REVERT: A 1943 ARG cc_start: 0.8282 (mpt180) cc_final: 0.7815 (mpt-90) REVERT: A 2215 GLN cc_start: 0.8342 (mm110) cc_final: 0.7900 (mt0) REVERT: A 2629 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7244 (mp0) REVERT: A 2763 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7786 (mmm160) REVERT: A 2869 ARG cc_start: 0.7435 (tpp-160) cc_final: 0.6634 (tpp-160) REVERT: A 3006 GLU cc_start: 0.7706 (tp30) cc_final: 0.7365 (tp30) REVERT: A 3043 MET cc_start: 0.7790 (pmm) cc_final: 0.7503 (pmm) REVERT: A 3169 MET cc_start: 0.8548 (mmp) cc_final: 0.8290 (mmp) REVERT: A 3196 GLU cc_start: 0.7936 (tt0) cc_final: 0.7339 (tp30) REVERT: A 3199 MET cc_start: 0.8109 (tmm) cc_final: 0.7757 (tmm) REVERT: A 3464 ASP cc_start: 0.4680 (OUTLIER) cc_final: 0.4326 (p0) REVERT: A 3695 ARG cc_start: 0.8931 (mtt-85) cc_final: 0.8139 (mtt-85) REVERT: A 3795 GLU cc_start: 0.7493 (tp30) cc_final: 0.7206 (tm-30) REVERT: A 3863 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8284 (tp) REVERT: A 3913 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: A 4231 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7539 (mm-40) REVERT: A 4292 LYS cc_start: 0.8191 (tttm) cc_final: 0.7832 (tttt) REVERT: A 4426 ASP cc_start: 0.7863 (t0) cc_final: 0.7633 (t0) REVERT: A 4547 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7501 (p) outliers start: 42 outliers final: 31 residues processed: 256 average time/residue: 0.3934 time to fit residues: 157.7550 Evaluate side-chains 247 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1840 SER Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2997 SER Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3464 ASP Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3913 GLU Chi-restraints excluded: chain A residue 3927 LEU Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4231 GLN Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4405 ILE Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4547 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 125 optimal weight: 0.0030 chunk 275 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 213 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107823 restraints weight = 31759.363| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.18 r_work: 0.3196 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23529 Z= 0.105 Angle : 0.480 9.342 31915 Z= 0.236 Chirality : 0.038 0.145 3595 Planarity : 0.004 0.054 4090 Dihedral : 5.235 86.005 3175 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.46 % Allowed : 14.30 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.16), residues: 2851 helix: 2.72 (0.13), residues: 1642 sheet: -0.43 (0.33), residues: 234 loop : 0.87 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.003 0.000 HIS A4006 PHE 0.019 0.001 PHE A3496 TYR 0.024 0.001 TYR A1546 ARG 0.005 0.000 ARG A3160 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 1364) hydrogen bonds : angle 3.65649 ( 3960) covalent geometry : bond 0.00233 (23529) covalent geometry : angle 0.47982 (31915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 2.465 Fit side-chains revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8925 (mtm) cc_final: 0.8722 (mtm) REVERT: A 1682 GLU cc_start: 0.8424 (tt0) cc_final: 0.8092 (tt0) REVERT: A 1694 GLU cc_start: 0.7517 (pm20) cc_final: 0.6525 (pm20) REVERT: A 1808 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8207 (mt) REVERT: A 1943 ARG cc_start: 0.8273 (mpt180) cc_final: 0.7869 (mpt-90) REVERT: A 2215 GLN cc_start: 0.8380 (mm110) cc_final: 0.8153 (tt0) REVERT: A 2629 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7355 (mp0) REVERT: A 2763 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7844 (mmm160) REVERT: A 2773 MET cc_start: 0.8957 (mtp) cc_final: 0.8757 (mtp) REVERT: A 2869 ARG cc_start: 0.7373 (tpp-160) cc_final: 0.6687 (tpp-160) REVERT: A 3169 MET cc_start: 0.8572 (mmp) cc_final: 0.8349 (mmp) REVERT: A 3196 GLU cc_start: 0.7919 (tt0) cc_final: 0.7350 (tp30) REVERT: A 3199 MET cc_start: 0.8071 (tmm) cc_final: 0.7761 (tmm) REVERT: A 3464 ASP cc_start: 0.4744 (OUTLIER) cc_final: 0.4310 (p0) REVERT: A 3524 MET cc_start: 0.8472 (tpp) cc_final: 0.8096 (tpt) REVERT: A 3695 ARG cc_start: 0.8946 (mtt-85) cc_final: 0.8211 (mtt-85) REVERT: A 3795 GLU cc_start: 0.7615 (tp30) cc_final: 0.7350 (tm-30) REVERT: A 3863 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8363 (tp) REVERT: A 3913 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7893 (mm-30) REVERT: A 4231 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7659 (mm-40) REVERT: A 4292 LYS cc_start: 0.8049 (tttm) cc_final: 0.7740 (tttt) REVERT: A 4344 LEU cc_start: 0.9064 (tp) cc_final: 0.8841 (tp) REVERT: A 4426 ASP cc_start: 0.7925 (t0) cc_final: 0.7720 (t0) REVERT: A 4547 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7608 (p) outliers start: 37 outliers final: 31 residues processed: 252 average time/residue: 0.3676 time to fit residues: 145.1167 Evaluate side-chains 249 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1840 SER Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2997 SER Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3464 ASP Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3913 GLU Chi-restraints excluded: chain A residue 3927 LEU Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4231 GLN Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4405 ILE Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4547 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 83 optimal weight: 0.0170 chunk 206 optimal weight: 0.9980 chunk 245 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.139647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108138 restraints weight = 31580.756| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.16 r_work: 0.3167 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23529 Z= 0.106 Angle : 0.476 7.230 31915 Z= 0.235 Chirality : 0.038 0.136 3595 Planarity : 0.004 0.054 4090 Dihedral : 5.192 89.039 3175 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.46 % Allowed : 14.38 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.16), residues: 2851 helix: 2.71 (0.13), residues: 1648 sheet: -0.56 (0.33), residues: 230 loop : 0.90 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2234 HIS 0.003 0.000 HIS A4006 PHE 0.012 0.001 PHE A2912 TYR 0.024 0.001 TYR A1546 ARG 0.005 0.000 ARG A3160 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1364) hydrogen bonds : angle 3.62954 ( 3960) covalent geometry : bond 0.00239 (23529) covalent geometry : angle 0.47573 (31915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13230.90 seconds wall clock time: 228 minutes 49.57 seconds (13729.57 seconds total)