Starting phenix.real_space_refine on Fri Jun 20 05:38:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dh7_46858/06_2025/9dh7_46858.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dh7_46858/06_2025/9dh7_46858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dh7_46858/06_2025/9dh7_46858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dh7_46858/06_2025/9dh7_46858.map" model { file = "/net/cci-nas-00/data/ceres_data/9dh7_46858/06_2025/9dh7_46858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dh7_46858/06_2025/9dh7_46858.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 14624 2.51 5 N 3977 2.21 5 O 4296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23020 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2857, 22907 Classifications: {'peptide': 2857} Link IDs: {'PTRANS': 130, 'TRANS': 2726} 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: 13.56, per 1000 atoms: 0.59 Number of scatterers: 23020 At special positions: 0 Unit cell: (124.988, 193.269, 150.449, 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 4296 8.00 N 3977 7.00 C 14624 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: 5.53 Conformation dependent library (CDL) restraints added in 2.8 seconds 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5430 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 17 sheets defined 63.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 1536 through 1554 Processing helix chain 'A' and resid 1561 through 1583 removed outlier: 3.542A pdb=" N SER A1583 " --> pdb=" O MET A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 removed outlier: 3.525A pdb=" N ASN A1593 " --> pdb=" O MET A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1625 removed outlier: 3.640A pdb=" N SER A1600 " --> pdb=" O GLY A1596 " (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 1653 removed outlier: 3.958A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.564A 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 1770 removed outlier: 3.571A pdb=" N VAL A1751 " --> pdb=" O ALA A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.860A 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 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' 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 1960 through 1963 Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.700A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (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 2150 through 2152 No H-bonds generated for 'chain 'A' and resid 2150 through 2152' Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 removed outlier: 3.901A 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: 3.851A 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 2293 through 2297 removed outlier: 3.518A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2308 through 2313 removed outlier: 3.627A pdb=" N GLU A2313 " --> pdb=" O PRO A2309 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2316 No H-bonds generated for 'chain 'A' and resid 2314 through 2316' Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.670A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) 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 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2431 through 2441 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.583A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) 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: 3.650A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.767A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.831A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.277A 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 2757 Processing helix chain 'A' and resid 2758 through 2764 removed outlier: 6.576A pdb=" N SER A2761 " --> pdb=" O LEU A2758 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.514A pdb=" N PHE A2776 " --> pdb=" O ALA A2772 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.780A 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: 4.032A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3062 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.685A pdb=" N LYS A3076 " --> pdb=" O SER A3072 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 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: 3.664A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3241 removed outlier: 3.587A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3495 removed outlier: 4.684A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A3495 " --> pdb=" O LYS A3491 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3517 removed outlier: 5.103A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.657A 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 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.514A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.649A 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: 3.558A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (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: 3.559A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A3797 " --> pdb=" O GLU A3793 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN A3800 " --> pdb=" O THR A3796 " (cutoff:3.500A) removed outlier: 4.134A 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: 3.616A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.695A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.584A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3894 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 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.185A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.536A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 removed outlier: 3.555A pdb=" N GLY A4014 " --> pdb=" O SER A4010 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.626A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.009A 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: 3.857A pdb=" N MET A4107 " --> pdb=" O PRO A4103 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.519A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.384A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 removed outlier: 3.525A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 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 4317 through 4322 Processing helix chain 'A' and resid 4326 through 4346 removed outlier: 4.356A pdb=" N VAL A4330 " --> pdb=" O ASN A4326 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A4331 " --> pdb=" O ALA A4327 " (cutoff:3.500A) Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.451A 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 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: 7.479A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.552A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1842 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 removed outlier: 6.573A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP A2304 " --> pdb=" O HIS A2252 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A2254 " --> pdb=" O ASP A2304 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) 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: 6.327A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 6.807A 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: 6.785A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.692A 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) removed outlier: 6.674A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 6.096A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.226A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.312A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.419A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.680A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.515A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1374 hydrogen bonds defined for protein. 4005 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: 13.69 Time building geometry restraints manager: 6.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7598 1.34 - 1.46: 5038 1.46 - 1.58: 10672 1.58 - 1.70: 14 1.70 - 1.82: 189 Bond restraints: 23511 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 2.99e+01 bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 ADP A4704 " pdb=" C6 ADP A4704 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 23506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 31557 2.58 - 5.15: 293 5.15 - 7.73: 27 7.73 - 10.30: 8 10.30 - 12.88: 7 Bond angle restraints: 31892 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 133.52 6.35 1.00e+00 1.00e+00 4.04e+01 angle pdb=" PA ATP A4702 " pdb=" O3A ATP A4702 " pdb=" PB ATP A4702 " ideal model delta sigma weight residual 136.83 131.14 5.69 1.00e+00 1.00e+00 3.23e+01 angle pdb=" PA ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sigma weight residual 120.50 133.38 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CA GLY A2740 " pdb=" C GLY A2740 " pdb=" O GLY A2740 " ideal model delta sigma weight residual 122.38 118.13 4.25 1.03e+00 9.43e-01 1.70e+01 angle pdb=" CA GLY A2740 " pdb=" C GLY A2740 " pdb=" N PRO A2741 " ideal model delta sigma weight residual 115.43 119.91 -4.48 1.17e+00 7.31e-01 1.46e+01 ... (remaining 31887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 13721 28.38 - 56.75: 465 56.75 - 85.13: 74 85.13 - 113.50: 6 113.50 - 141.88: 3 Dihedral angle restraints: 14269 sinusoidal: 5908 harmonic: 8361 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 81.87 -141.88 1 2.00e+01 2.50e-03 4.29e+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 300.00 166.83 133.17 1 2.00e+01 2.50e-03 4.04e+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 300.00 169.02 130.98 1 2.00e+01 2.50e-03 3.97e+01 ... (remaining 14266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3013 0.055 - 0.109: 502 0.109 - 0.164: 66 0.164 - 0.218: 10 0.218 - 0.273: 2 Chirality restraints: 3593 Sorted by residual: chirality pdb=" CB THR A4267 " pdb=" CA THR A4267 " pdb=" OG1 THR A4267 " pdb=" CG2 THR A4267 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE A2049 " pdb=" N ILE A2049 " pdb=" C ILE A2049 " pdb=" CB ILE A2049 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 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 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 3590 not shown) Planarity restraints: 4087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2801 " 0.273 9.50e-02 1.11e+02 1.22e-01 9.20e+00 pdb=" NE ARG A2801 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A2801 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A2801 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A2801 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2025 " 0.168 9.50e-02 1.11e+02 7.53e-02 3.49e+00 pdb=" NE ARG A2025 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A2025 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A2025 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A2025 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A3136 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A3137 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A3137 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A3137 " -0.024 5.00e-02 4.00e+02 ... (remaining 4084 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 86 2.49 - 3.09: 16448 3.09 - 3.70: 36019 3.70 - 4.30: 54057 4.30 - 4.90: 88500 Nonbonded interactions: 195110 Sorted by model distance: nonbonded pdb=" OG SER A2231 " pdb="MG MG A4705 " model vdw 1.891 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4705 " model vdw 2.047 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4705 " model vdw 2.142 2.170 nonbonded pdb=" OH TYR A2967 " pdb=" OD2 ASP A2975 " model vdw 2.185 3.040 nonbonded pdb=" OG1 THR A2627 " pdb=" OE1 GLU A2629 " model vdw 2.215 3.040 ... (remaining 195105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.850 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: 0.040 Extract box with map and model: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 58.530 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 23511 Z= 0.234 Angle : 0.632 12.876 31892 Z= 0.355 Chirality : 0.042 0.273 3593 Planarity : 0.005 0.122 4087 Dihedral : 14.469 141.878 8839 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.04 % Allowed : 0.28 % Favored : 99.68 % 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: 2.13 (0.16), residues: 2849 helix: 2.09 (0.13), residues: 1633 sheet: 0.01 (0.33), residues: 252 loop : 0.78 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1701 HIS 0.006 0.001 HIS A1810 PHE 0.017 0.001 PHE A1926 TYR 0.027 0.001 TYR A1546 ARG 0.009 0.000 ARG A1966 Details of bonding type rmsd hydrogen bonds : bond 0.12354 ( 1374) hydrogen bonds : angle 5.35418 ( 4005) covalent geometry : bond 0.00395 (23511) covalent geometry : angle 0.63151 (31892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 637 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2976 LEU cc_start: 0.8092 (mt) cc_final: 0.7832 (mt) REVERT: A 3124 ASP cc_start: 0.6819 (p0) cc_final: 0.6561 (p0) REVERT: A 3584 ASN cc_start: 0.7462 (m110) cc_final: 0.6957 (m110) REVERT: A 3691 ASP cc_start: 0.7226 (p0) cc_final: 0.6970 (p0) REVERT: A 3704 THR cc_start: 0.8583 (p) cc_final: 0.8313 (p) REVERT: A 4398 LEU cc_start: 0.7319 (mt) cc_final: 0.7112 (mp) outliers start: 1 outliers final: 1 residues processed: 638 average time/residue: 0.4466 time to fit residues: 418.1182 Evaluate side-chains 267 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2321 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 73 optimal weight: 0.0050 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 258 optimal weight: 0.4980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1653 HIS A1856 GLN A1985 HIS ** A2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2621 ASN A2827 HIS A3631 ASN A3650 ASN ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4078 ASN A4098 ASN A4335 GLN A4466 HIS A4477 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.101072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080524 restraints weight = 57263.514| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.18 r_work: 0.3140 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23511 Z= 0.130 Angle : 0.581 7.950 31892 Z= 0.288 Chirality : 0.041 0.294 3593 Planarity : 0.004 0.047 4087 Dihedral : 7.103 144.141 3175 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.54 % Allowed : 8.34 % Favored : 90.12 % 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: 2.36 (0.16), residues: 2849 helix: 2.31 (0.13), residues: 1647 sheet: -0.20 (0.33), residues: 243 loop : 0.87 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1701 HIS 0.004 0.001 HIS A1695 PHE 0.031 0.001 PHE A2479 TYR 0.024 0.001 TYR A1546 ARG 0.007 0.001 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 1374) hydrogen bonds : angle 4.29647 ( 4005) covalent geometry : bond 0.00282 (23511) covalent geometry : angle 0.58090 (31892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8811 (mtp) cc_final: 0.8290 (mpp) REVERT: A 1697 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7970 (mmmt) REVERT: A 1987 ASN cc_start: 0.6526 (OUTLIER) cc_final: 0.6317 (p0) REVERT: A 2011 ASP cc_start: 0.8344 (m-30) cc_final: 0.7802 (m-30) REVERT: A 2041 MET cc_start: 0.8575 (mtm) cc_final: 0.8198 (mtp) REVERT: A 2143 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8382 (mm-30) REVERT: A 2202 MET cc_start: 0.8655 (mmm) cc_final: 0.8401 (ttm) REVERT: A 2221 MET cc_start: 0.8899 (mtp) cc_final: 0.8693 (mtp) REVERT: A 2510 MET cc_start: 0.8770 (mmm) cc_final: 0.8280 (mmm) REVERT: A 2755 MET cc_start: 0.9247 (ttp) cc_final: 0.9011 (ttm) REVERT: A 3124 ASP cc_start: 0.7993 (p0) cc_final: 0.7664 (p0) REVERT: A 3183 TYR cc_start: 0.9339 (t80) cc_final: 0.8995 (t80) REVERT: A 3218 LEU cc_start: 0.6840 (mm) cc_final: 0.6631 (tp) REVERT: A 3524 MET cc_start: 0.8992 (tpt) cc_final: 0.8736 (tpt) REVERT: A 3557 ASP cc_start: 0.8971 (m-30) cc_final: 0.8032 (p0) REVERT: A 3737 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8393 (tm-30) REVERT: A 3751 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8571 (tp-100) REVERT: A 3791 MET cc_start: 0.8287 (mmm) cc_final: 0.7879 (mmm) REVERT: A 3834 ASP cc_start: 0.9023 (m-30) cc_final: 0.8716 (m-30) REVERT: A 4022 GLU cc_start: 0.8541 (pp20) cc_final: 0.8266 (pp20) REVERT: A 4057 ASP cc_start: 0.8677 (m-30) cc_final: 0.8468 (m-30) REVERT: A 4217 ASP cc_start: 0.9246 (OUTLIER) cc_final: 0.8989 (m-30) REVERT: A 4279 ASP cc_start: 0.8227 (m-30) cc_final: 0.7974 (m-30) REVERT: A 4377 MET cc_start: 0.7765 (mtt) cc_final: 0.7317 (mtm) REVERT: A 4457 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8357 (mtmt) REVERT: A 4473 MET cc_start: 0.8633 (ttm) cc_final: 0.8081 (ttm) outliers start: 39 outliers final: 20 residues processed: 315 average time/residue: 0.3944 time to fit residues: 195.7561 Evaluate side-chains 234 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1987 ASN Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2540 SER Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3910 ARG Chi-restraints excluded: chain A residue 4159 ARG Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4217 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4477 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 250 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1779 HIS ** A2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS A3181 ASN ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3820 GLN A4386 ASN A4477 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074165 restraints weight = 58190.470| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.03 r_work: 0.3011 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23511 Z= 0.230 Angle : 0.622 8.939 31892 Z= 0.311 Chirality : 0.042 0.262 3593 Planarity : 0.004 0.043 4087 Dihedral : 7.008 138.591 3173 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.53 % Allowed : 9.72 % Favored : 87.75 % 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: 2.13 (0.16), residues: 2849 helix: 2.21 (0.13), residues: 1646 sheet: -0.54 (0.31), residues: 266 loop : 0.69 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1701 HIS 0.006 0.001 HIS A2857 PHE 0.016 0.002 PHE A2364 TYR 0.023 0.002 TYR A1546 ARG 0.006 0.001 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 1374) hydrogen bonds : angle 4.19278 ( 4005) covalent geometry : bond 0.00534 (23511) covalent geometry : angle 0.62185 (31892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 214 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8892 (mtp) cc_final: 0.8468 (mpp) REVERT: A 1697 LYS cc_start: 0.8479 (mtmm) cc_final: 0.8037 (mmmt) REVERT: A 2011 ASP cc_start: 0.8332 (m-30) cc_final: 0.7868 (m-30) REVERT: A 2221 MET cc_start: 0.8832 (mtp) cc_final: 0.8471 (mtp) REVERT: A 2455 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8663 (mm) REVERT: A 2603 MET cc_start: 0.9096 (ttp) cc_final: 0.8547 (ptm) REVERT: A 2755 MET cc_start: 0.9353 (ttp) cc_final: 0.9139 (ttm) REVERT: A 3115 LEU cc_start: 0.8903 (mt) cc_final: 0.8619 (mt) REVERT: A 3124 ASP cc_start: 0.7936 (p0) cc_final: 0.7519 (p0) REVERT: A 3183 TYR cc_start: 0.9320 (t80) cc_final: 0.9051 (t80) REVERT: A 3751 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8370 (tp-100) REVERT: A 3791 MET cc_start: 0.8356 (mmm) cc_final: 0.8056 (mmm) REVERT: A 3834 ASP cc_start: 0.9001 (m-30) cc_final: 0.8623 (m-30) REVERT: A 3910 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8626 (ptp-110) REVERT: A 3946 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7807 (p0) REVERT: A 4022 GLU cc_start: 0.8712 (pp20) cc_final: 0.8369 (pp20) REVERT: A 4057 ASP cc_start: 0.8696 (m-30) cc_final: 0.8401 (m-30) REVERT: A 4217 ASP cc_start: 0.9280 (OUTLIER) cc_final: 0.9063 (m-30) REVERT: A 4287 LYS cc_start: 0.7956 (tptp) cc_final: 0.7353 (mmtt) REVERT: A 4457 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8443 (mtmt) outliers start: 64 outliers final: 31 residues processed: 264 average time/residue: 0.3903 time to fit residues: 165.7662 Evaluate side-chains 224 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2038 SER Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2197 GLU Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3709 GLN Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3910 ARG Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4049 TYR Chi-restraints excluded: chain A residue 4063 ASN Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4217 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4623 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 37 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 137 optimal weight: 0.0030 chunk 227 optimal weight: 4.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2707 GLN A2954 ASN A3667 GLN ** A3735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3837 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.095585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.075650 restraints weight = 58047.628| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.09 r_work: 0.3052 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23511 Z= 0.127 Angle : 0.536 10.927 31892 Z= 0.263 Chirality : 0.040 0.214 3593 Planarity : 0.004 0.041 4087 Dihedral : 6.803 135.819 3173 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.94 % Allowed : 11.15 % Favored : 86.92 % 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: 2.28 (0.16), residues: 2849 helix: 2.36 (0.13), residues: 1649 sheet: -0.42 (0.32), residues: 261 loop : 0.66 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1701 HIS 0.006 0.001 HIS A3837 PHE 0.010 0.001 PHE A3813 TYR 0.022 0.001 TYR A1546 ARG 0.004 0.000 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1374) hydrogen bonds : angle 3.96658 ( 4005) covalent geometry : bond 0.00286 (23511) covalent geometry : angle 0.53587 (31892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 4.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8393 (mpp) REVERT: A 1677 SER cc_start: 0.8811 (t) cc_final: 0.8478 (m) REVERT: A 1697 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8092 (mmmt) REVERT: A 1948 LEU cc_start: 0.9123 (mp) cc_final: 0.8900 (mt) REVERT: A 2011 ASP cc_start: 0.8288 (m-30) cc_final: 0.7870 (m-30) REVERT: A 2221 MET cc_start: 0.8806 (mtp) cc_final: 0.8549 (mtp) REVERT: A 2455 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8629 (mm) REVERT: A 2471 GLN cc_start: 0.8945 (tt0) cc_final: 0.8623 (tp-100) REVERT: A 2603 MET cc_start: 0.9038 (ttp) cc_final: 0.8539 (ptm) REVERT: A 2755 MET cc_start: 0.9350 (ttp) cc_final: 0.9143 (ttm) REVERT: A 3124 ASP cc_start: 0.7877 (p0) cc_final: 0.7507 (p0) REVERT: A 3183 TYR cc_start: 0.9246 (t80) cc_final: 0.8958 (t80) REVERT: A 3598 GLU cc_start: 0.9029 (mp0) cc_final: 0.8764 (mp0) REVERT: A 3751 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8436 (tp-100) REVERT: A 3791 MET cc_start: 0.8384 (mmm) cc_final: 0.7997 (mmm) REVERT: A 3834 ASP cc_start: 0.9018 (m-30) cc_final: 0.8676 (m-30) REVERT: A 4057 ASP cc_start: 0.8720 (m-30) cc_final: 0.8473 (m-30) REVERT: A 4276 ARG cc_start: 0.8800 (mmp80) cc_final: 0.8595 (mmm160) REVERT: A 4457 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8388 (mtmt) REVERT: A 4473 MET cc_start: 0.8705 (ttm) cc_final: 0.8326 (ttm) outliers start: 49 outliers final: 35 residues processed: 259 average time/residue: 0.5260 time to fit residues: 227.7521 Evaluate side-chains 228 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 5.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2038 SER Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2197 GLU Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3709 GLN Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4049 TYR Chi-restraints excluded: chain A residue 4159 ARG Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4494 LEU Chi-restraints excluded: chain A residue 4623 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 207 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 259 optimal weight: 0.5980 chunk 160 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2079 GLN ** A2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3563 GLN A3667 GLN A3735 GLN A4065 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.095695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075660 restraints weight = 58110.682| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.12 r_work: 0.3051 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23511 Z= 0.115 Angle : 0.520 8.361 31892 Z= 0.255 Chirality : 0.039 0.234 3593 Planarity : 0.004 0.042 4087 Dihedral : 6.633 131.736 3173 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.82 % Allowed : 12.25 % Favored : 85.93 % 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: 2.33 (0.16), residues: 2849 helix: 2.39 (0.13), residues: 1655 sheet: -0.46 (0.32), residues: 263 loop : 0.73 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1701 HIS 0.009 0.001 HIS A3837 PHE 0.010 0.001 PHE A3813 TYR 0.022 0.001 TYR A1546 ARG 0.006 0.000 ARG A3910 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 1374) hydrogen bonds : angle 3.88545 ( 4005) covalent geometry : bond 0.00254 (23511) covalent geometry : angle 0.51986 (31892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8397 (mpp) REVERT: A 1677 SER cc_start: 0.8808 (t) cc_final: 0.8476 (m) REVERT: A 1697 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8137 (mmmt) REVERT: A 1892 MET cc_start: 0.9004 (mmp) cc_final: 0.8518 (mmp) REVERT: A 2011 ASP cc_start: 0.8125 (m-30) cc_final: 0.7764 (m-30) REVERT: A 2221 MET cc_start: 0.8769 (mtp) cc_final: 0.8548 (mtp) REVERT: A 2265 TYR cc_start: 0.8674 (m-10) cc_final: 0.8463 (m-10) REVERT: A 2455 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8712 (mm) REVERT: A 2471 GLN cc_start: 0.8963 (tt0) cc_final: 0.8637 (tp-100) REVERT: A 2503 SER cc_start: 0.8979 (p) cc_final: 0.8740 (t) REVERT: A 2603 MET cc_start: 0.9047 (ttp) cc_final: 0.8567 (ptm) REVERT: A 2755 MET cc_start: 0.9365 (ttp) cc_final: 0.9153 (ttm) REVERT: A 3113 MET cc_start: 0.8811 (ptp) cc_final: 0.8318 (ptp) REVERT: A 3115 LEU cc_start: 0.8900 (mt) cc_final: 0.8622 (mt) REVERT: A 3124 ASP cc_start: 0.7888 (p0) cc_final: 0.7495 (p0) REVERT: A 3183 TYR cc_start: 0.9267 (t80) cc_final: 0.8964 (t80) REVERT: A 3598 GLU cc_start: 0.9007 (mp0) cc_final: 0.8734 (mp0) REVERT: A 3751 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8418 (tp-100) REVERT: A 3791 MET cc_start: 0.8445 (mmm) cc_final: 0.8030 (mmm) REVERT: A 3834 ASP cc_start: 0.9017 (m-30) cc_final: 0.8668 (m-30) REVERT: A 4010 SER cc_start: 0.8930 (m) cc_final: 0.8707 (p) REVERT: A 4057 ASP cc_start: 0.8705 (m-30) cc_final: 0.8446 (m-30) REVERT: A 4276 ARG cc_start: 0.8791 (mmp80) cc_final: 0.8452 (mmp80) REVERT: A 4457 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8381 (mtmt) REVERT: A 4473 MET cc_start: 0.8665 (ttm) cc_final: 0.8043 (ttm) outliers start: 46 outliers final: 35 residues processed: 244 average time/residue: 0.3606 time to fit residues: 142.6730 Evaluate side-chains 227 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2038 SER Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2197 GLU Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3709 GLN Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4049 TYR Chi-restraints excluded: chain A residue 4159 ARG Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4494 LEU Chi-restraints excluded: chain A residue 4623 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 260 optimal weight: 6.9990 chunk 218 optimal weight: 0.0270 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 173 optimal weight: 0.4980 chunk 192 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 GLN A2079 GLN ** A2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3667 GLN A3837 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.094399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074492 restraints weight = 58028.275| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.10 r_work: 0.3025 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23511 Z= 0.145 Angle : 0.533 8.336 31892 Z= 0.263 Chirality : 0.040 0.222 3593 Planarity : 0.004 0.042 4087 Dihedral : 6.431 128.165 3173 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.82 % Allowed : 12.29 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.33 (0.16), residues: 2849 helix: 2.39 (0.13), residues: 1657 sheet: -0.41 (0.33), residues: 245 loop : 0.67 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1701 HIS 0.006 0.001 HIS A2857 PHE 0.010 0.001 PHE A3813 TYR 0.022 0.001 TYR A1546 ARG 0.008 0.000 ARG A3167 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1374) hydrogen bonds : angle 3.85883 ( 4005) covalent geometry : bond 0.00333 (23511) covalent geometry : angle 0.53333 (31892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8403 (mpp) REVERT: A 1677 SER cc_start: 0.8754 (t) cc_final: 0.8450 (m) REVERT: A 1697 LYS cc_start: 0.8442 (mtmm) cc_final: 0.8233 (mmmt) REVERT: A 2011 ASP cc_start: 0.8272 (m-30) cc_final: 0.8024 (m-30) REVERT: A 2221 MET cc_start: 0.8814 (mtp) cc_final: 0.8599 (mtp) REVERT: A 2455 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8735 (mm) REVERT: A 2471 GLN cc_start: 0.8913 (tt0) cc_final: 0.8540 (tp-100) REVERT: A 2503 SER cc_start: 0.8974 (p) cc_final: 0.8756 (t) REVERT: A 2603 MET cc_start: 0.9059 (ttp) cc_final: 0.8594 (ptm) REVERT: A 3115 LEU cc_start: 0.8975 (mt) cc_final: 0.8719 (mt) REVERT: A 3124 ASP cc_start: 0.7918 (p0) cc_final: 0.7522 (p0) REVERT: A 3183 TYR cc_start: 0.9268 (t80) cc_final: 0.8958 (t80) REVERT: A 3598 GLU cc_start: 0.8969 (mp0) cc_final: 0.8724 (mp0) REVERT: A 3751 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8430 (tp-100) REVERT: A 3791 MET cc_start: 0.8488 (mmm) cc_final: 0.8056 (mmm) REVERT: A 3834 ASP cc_start: 0.9011 (m-30) cc_final: 0.8693 (m-30) REVERT: A 4010 SER cc_start: 0.9029 (m) cc_final: 0.8816 (p) REVERT: A 4057 ASP cc_start: 0.8711 (m-30) cc_final: 0.8464 (m-30) REVERT: A 4276 ARG cc_start: 0.8808 (mmp80) cc_final: 0.8512 (mmp80) REVERT: A 4343 MET cc_start: 0.8794 (mtp) cc_final: 0.8539 (mtt) REVERT: A 4457 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8437 (mtmt) REVERT: A 4459 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8597 (tp) outliers start: 46 outliers final: 35 residues processed: 233 average time/residue: 0.3522 time to fit residues: 133.9769 Evaluate side-chains 220 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2038 SER Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2197 GLU Chi-restraints excluded: chain A residue 2410 SER Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2513 GLU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2655 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3709 GLN Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4049 TYR Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4494 LEU Chi-restraints excluded: chain A residue 4623 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 277 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 267 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2079 GLN ** A2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2439 HIS A2849 ASN A3667 GLN A3837 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.095423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.075810 restraints weight = 58223.594| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.09 r_work: 0.3052 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23511 Z= 0.109 Angle : 0.515 9.372 31892 Z= 0.251 Chirality : 0.039 0.252 3593 Planarity : 0.003 0.042 4087 Dihedral : 6.308 124.615 3173 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.58 % Allowed : 13.04 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.16), residues: 2849 helix: 2.47 (0.13), residues: 1657 sheet: -0.50 (0.32), residues: 255 loop : 0.71 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1701 HIS 0.012 0.001 HIS A3837 PHE 0.012 0.001 PHE A2479 TYR 0.022 0.001 TYR A1546 ARG 0.006 0.000 ARG A3167 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1374) hydrogen bonds : angle 3.77615 ( 4005) covalent geometry : bond 0.00241 (23511) covalent geometry : angle 0.51510 (31892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8375 (mpp) REVERT: A 1677 SER cc_start: 0.8745 (t) cc_final: 0.8440 (m) REVERT: A 2221 MET cc_start: 0.8803 (mtp) cc_final: 0.8582 (mtp) REVERT: A 2342 MET cc_start: 0.8101 (mtt) cc_final: 0.7780 (ptp) REVERT: A 2455 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8753 (mm) REVERT: A 2471 GLN cc_start: 0.8908 (tt0) cc_final: 0.8551 (tp-100) REVERT: A 2603 MET cc_start: 0.9036 (ttp) cc_final: 0.8573 (ptm) REVERT: A 3115 LEU cc_start: 0.8945 (mt) cc_final: 0.8704 (mt) REVERT: A 3124 ASP cc_start: 0.7884 (p0) cc_final: 0.7517 (p0) REVERT: A 3183 TYR cc_start: 0.9266 (t80) cc_final: 0.8964 (t80) REVERT: A 3598 GLU cc_start: 0.8967 (mp0) cc_final: 0.8716 (mp0) REVERT: A 3751 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8438 (tp-100) REVERT: A 3791 MET cc_start: 0.8535 (mmm) cc_final: 0.8113 (mmm) REVERT: A 3834 ASP cc_start: 0.8995 (m-30) cc_final: 0.8760 (m-30) REVERT: A 4057 ASP cc_start: 0.8705 (m-30) cc_final: 0.8450 (m-30) REVERT: A 4276 ARG cc_start: 0.8817 (mmp80) cc_final: 0.8601 (mmp80) REVERT: A 4343 MET cc_start: 0.8685 (mtp) cc_final: 0.8383 (mtt) REVERT: A 4457 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8422 (mtmt) REVERT: A 4459 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8565 (tp) REVERT: A 4473 MET cc_start: 0.8675 (ttm) cc_final: 0.8175 (ttm) outliers start: 40 outliers final: 27 residues processed: 234 average time/residue: 0.3561 time to fit residues: 134.2640 Evaluate side-chains 215 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2038 SER Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2197 GLU Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3100 GLU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4049 TYR Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4623 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 278 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2079 GLN ** A2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS A3667 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.092778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.073332 restraints weight = 58643.390| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.05 r_work: 0.3004 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23511 Z= 0.186 Angle : 0.574 8.877 31892 Z= 0.282 Chirality : 0.041 0.214 3593 Planarity : 0.004 0.041 4087 Dihedral : 6.276 122.435 3173 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.62 % Allowed : 13.32 % Favored : 85.06 % 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: 2.24 (0.16), residues: 2849 helix: 2.34 (0.13), residues: 1659 sheet: -0.49 (0.32), residues: 248 loop : 0.61 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.005 0.001 HIS A2857 PHE 0.016 0.001 PHE A2479 TYR 0.023 0.001 TYR A1546 ARG 0.005 0.000 ARG A3167 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 1374) hydrogen bonds : angle 3.90588 ( 4005) covalent geometry : bond 0.00430 (23511) covalent geometry : angle 0.57354 (31892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8388 (mpp) REVERT: A 1694 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7037 (tp30) REVERT: A 1892 MET cc_start: 0.9026 (mmp) cc_final: 0.8613 (mmp) REVERT: A 2221 MET cc_start: 0.8831 (mtp) cc_final: 0.8595 (mtp) REVERT: A 2455 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8765 (mm) REVERT: A 2471 GLN cc_start: 0.8950 (tt0) cc_final: 0.8570 (tp-100) REVERT: A 2478 ASP cc_start: 0.7501 (p0) cc_final: 0.7201 (p0) REVERT: A 2603 MET cc_start: 0.9072 (ttp) cc_final: 0.8614 (ptm) REVERT: A 2755 MET cc_start: 0.9355 (ttp) cc_final: 0.9145 (ttm) REVERT: A 3115 LEU cc_start: 0.8969 (mt) cc_final: 0.8744 (mt) REVERT: A 3124 ASP cc_start: 0.7940 (p0) cc_final: 0.7576 (p0) REVERT: A 3183 TYR cc_start: 0.9256 (t80) cc_final: 0.8939 (t80) REVERT: A 3751 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8524 (tp-100) REVERT: A 3791 MET cc_start: 0.8508 (mmm) cc_final: 0.8078 (mmm) REVERT: A 3834 ASP cc_start: 0.9019 (m-30) cc_final: 0.8770 (m-30) REVERT: A 4057 ASP cc_start: 0.8704 (m-30) cc_final: 0.8448 (m-30) REVERT: A 4276 ARG cc_start: 0.8856 (mmp80) cc_final: 0.8643 (mmp80) REVERT: A 4343 MET cc_start: 0.8763 (mtp) cc_final: 0.8453 (mtt) REVERT: A 4457 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8501 (mtmt) REVERT: A 4459 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8649 (tp) REVERT: A 4597 ASN cc_start: 0.7820 (m110) cc_final: 0.7555 (m-40) outliers start: 41 outliers final: 32 residues processed: 221 average time/residue: 0.3796 time to fit residues: 138.2367 Evaluate side-chains 210 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2038 SER Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2197 GLU Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3100 GLU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3528 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3709 GLN Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4049 TYR Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4623 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 37 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 99 optimal weight: 0.0010 chunk 235 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2316 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 = 0.3483 r_free = 0.3483 target = 0.093283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.073904 restraints weight = 58447.061| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.06 r_work: 0.3011 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23511 Z= 0.159 Angle : 0.563 12.683 31892 Z= 0.277 Chirality : 0.040 0.211 3593 Planarity : 0.004 0.041 4087 Dihedral : 6.214 119.463 3173 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.50 % Allowed : 13.44 % Favored : 85.06 % 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: 2.21 (0.16), residues: 2849 helix: 2.34 (0.13), residues: 1662 sheet: -0.52 (0.32), residues: 247 loop : 0.55 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1701 HIS 0.004 0.001 HIS A2857 PHE 0.013 0.001 PHE A2479 TYR 0.023 0.001 TYR A1546 ARG 0.005 0.000 ARG A3167 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 1374) hydrogen bonds : angle 3.86110 ( 4005) covalent geometry : bond 0.00367 (23511) covalent geometry : angle 0.56285 (31892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8418 (mpp) REVERT: A 1677 SER cc_start: 0.8813 (t) cc_final: 0.8488 (m) REVERT: A 1694 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7083 (tp30) REVERT: A 1892 MET cc_start: 0.9021 (mmp) cc_final: 0.8572 (mmp) REVERT: A 2221 MET cc_start: 0.8783 (mtp) cc_final: 0.8560 (mtp) REVERT: A 2455 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 2471 GLN cc_start: 0.8945 (tt0) cc_final: 0.8561 (tp-100) REVERT: A 2603 MET cc_start: 0.9065 (ttp) cc_final: 0.8621 (ptm) REVERT: A 2755 MET cc_start: 0.9350 (ttp) cc_final: 0.9125 (ttm) REVERT: A 3114 ASP cc_start: 0.8334 (t70) cc_final: 0.8113 (p0) REVERT: A 3124 ASP cc_start: 0.7930 (p0) cc_final: 0.7609 (p0) REVERT: A 3183 TYR cc_start: 0.9233 (t80) cc_final: 0.8938 (t80) REVERT: A 3751 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8415 (tp-100) REVERT: A 3791 MET cc_start: 0.8498 (mmm) cc_final: 0.7867 (mmm) REVERT: A 3795 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8551 (mm-30) REVERT: A 3834 ASP cc_start: 0.9016 (m-30) cc_final: 0.8772 (m-30) REVERT: A 4057 ASP cc_start: 0.8698 (m-30) cc_final: 0.8442 (m-30) REVERT: A 4276 ARG cc_start: 0.8853 (mmp80) cc_final: 0.8599 (mmp80) REVERT: A 4343 MET cc_start: 0.8763 (mtp) cc_final: 0.8445 (mtt) REVERT: A 4457 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8456 (mtmt) REVERT: A 4459 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8656 (tp) REVERT: A 4473 MET cc_start: 0.8658 (ttm) cc_final: 0.8157 (ttm) REVERT: A 4597 ASN cc_start: 0.7870 (m110) cc_final: 0.7572 (m-40) outliers start: 38 outliers final: 32 residues processed: 211 average time/residue: 0.3342 time to fit residues: 115.1786 Evaluate side-chains 208 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2197 GLU Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3100 GLU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3528 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3709 GLN Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4049 TYR Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4443 LYS Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4623 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 87 optimal weight: 0.1980 chunk 124 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 279 optimal weight: 0.2980 chunk 203 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2079 GLN ** A2316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.095380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076026 restraints weight = 58424.292| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.11 r_work: 0.3056 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23511 Z= 0.104 Angle : 0.538 11.159 31892 Z= 0.262 Chirality : 0.039 0.263 3593 Planarity : 0.004 0.042 4087 Dihedral : 6.041 114.631 3173 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.07 % Allowed : 13.79 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.38 (0.16), residues: 2849 helix: 2.47 (0.13), residues: 1657 sheet: -0.51 (0.33), residues: 246 loop : 0.64 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1701 HIS 0.006 0.001 HIS A2445 PHE 0.011 0.001 PHE A2949 TYR 0.023 0.001 TYR A1546 ARG 0.005 0.000 ARG A3167 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 1374) hydrogen bonds : angle 3.71355 ( 4005) covalent geometry : bond 0.00226 (23511) covalent geometry : angle 0.53839 (31892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8367 (mpp) REVERT: A 1677 SER cc_start: 0.8770 (t) cc_final: 0.8477 (m) REVERT: A 1892 MET cc_start: 0.8994 (mmp) cc_final: 0.8638 (mmp) REVERT: A 2004 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8133 (mttt) REVERT: A 2018 MET cc_start: 0.8156 (ptm) cc_final: 0.7901 (mtm) REVERT: A 2221 MET cc_start: 0.8696 (mtp) cc_final: 0.8467 (mtp) REVERT: A 2310 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8692 (mm-30) REVERT: A 2412 MET cc_start: 0.8037 (tpp) cc_final: 0.7745 (tmm) REVERT: A 2471 GLN cc_start: 0.8926 (tt0) cc_final: 0.8582 (tp-100) REVERT: A 2510 MET cc_start: 0.8464 (mmm) cc_final: 0.7670 (mmm) REVERT: A 2603 MET cc_start: 0.9032 (ttp) cc_final: 0.8602 (ptm) REVERT: A 2755 MET cc_start: 0.9380 (ttp) cc_final: 0.9151 (ttm) REVERT: A 3109 PHE cc_start: 0.8503 (t80) cc_final: 0.8271 (t80) REVERT: A 3124 ASP cc_start: 0.7944 (p0) cc_final: 0.7619 (p0) REVERT: A 3183 TYR cc_start: 0.9208 (t80) cc_final: 0.8923 (t80) REVERT: A 3196 GLU cc_start: 0.8366 (tp30) cc_final: 0.8112 (tp30) REVERT: A 3751 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8464 (tp-100) REVERT: A 3791 MET cc_start: 0.8459 (mmm) cc_final: 0.7966 (mmm) REVERT: A 3834 ASP cc_start: 0.8977 (m-30) cc_final: 0.8743 (m-30) REVERT: A 4049 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7241 (t80) REVERT: A 4057 ASP cc_start: 0.8717 (m-30) cc_final: 0.8465 (m-30) REVERT: A 4081 ASP cc_start: 0.8640 (t0) cc_final: 0.8337 (t0) REVERT: A 4085 ASN cc_start: 0.8690 (m-40) cc_final: 0.8241 (m110) REVERT: A 4192 GLU cc_start: 0.8795 (tp30) cc_final: 0.8564 (mm-30) REVERT: A 4247 MET cc_start: 0.9152 (mtp) cc_final: 0.8811 (mtm) REVERT: A 4276 ARG cc_start: 0.8843 (mmp80) cc_final: 0.8568 (mmp80) REVERT: A 4459 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8586 (tp) REVERT: A 4473 MET cc_start: 0.8532 (ttm) cc_final: 0.8008 (ttm) REVERT: A 4597 ASN cc_start: 0.7873 (m110) cc_final: 0.7617 (m110) outliers start: 27 outliers final: 23 residues processed: 227 average time/residue: 0.3414 time to fit residues: 128.4367 Evaluate side-chains 210 residues out of total 2530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2197 GLU Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3100 GLU Chi-restraints excluded: chain A residue 3528 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4049 TYR Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4459 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 216 optimal weight: 0.6980 chunk 111 optimal weight: 0.0020 chunk 256 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 54 optimal weight: 0.0570 chunk 226 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.076446 restraints weight = 58223.610| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.13 r_work: 0.3068 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23511 Z= 0.101 Angle : 0.541 11.037 31892 Z= 0.262 Chirality : 0.039 0.274 3593 Planarity : 0.004 0.045 4087 Dihedral : 5.914 111.102 3173 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.11 % Allowed : 13.75 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.44 (0.16), residues: 2849 helix: 2.50 (0.13), residues: 1662 sheet: -0.41 (0.33), residues: 243 loop : 0.68 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1701 HIS 0.004 0.000 HIS A2857 PHE 0.009 0.001 PHE A2343 TYR 0.024 0.001 TYR A1546 ARG 0.005 0.000 ARG A3167 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 1374) hydrogen bonds : angle 3.68502 ( 4005) covalent geometry : bond 0.00218 (23511) covalent geometry : angle 0.54137 (31892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11735.62 seconds wall clock time: 203 minutes 50.46 seconds (12230.46 seconds total)