Starting phenix.real_space_refine on Sat May 24 05:18:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bn1_44718/05_2025/9bn1_44718.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bn1_44718/05_2025/9bn1_44718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bn1_44718/05_2025/9bn1_44718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bn1_44718/05_2025/9bn1_44718.map" model { file = "/net/cci-nas-00/data/ceres_data/9bn1_44718/05_2025/9bn1_44718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bn1_44718/05_2025/9bn1_44718.cif" } resolution = 3.8 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= 0.028 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 7 5.49 5 Mg 1 5.21 5 S 122 5.16 5 C 15572 2.51 5 N 4223 2.21 5 O 4551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24476 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3029, 24390 Classifications: {'peptide': 3029} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2895} Chain breaks: 4 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' MG': 1, 'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 13.26, per 1000 atoms: 0.54 Number of scatterers: 24476 At special positions: 0 Unit cell: (122.388, 165.354, 174.468, 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 122 16.00 P 7 15.00 Mg 1 11.99 O 4551 8.00 N 4223 7.00 C 15572 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: 5.92 Conformation dependent library (CDL) restraints added in 3.1 seconds 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 21 sheets defined 64.6% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 removed outlier: 4.093A pdb=" N LYS A1338 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A1339 " --> pdb=" O GLU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1372 Processing helix chain 'A' and resid 1374 through 1379 Processing helix chain 'A' and resid 1380 through 1404 removed outlier: 3.611A pdb=" N GLU A1384 " --> pdb=" O TYR A1380 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A1398 " --> pdb=" O MET A1394 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU A1399 " --> pdb=" O LYS A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1421 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.629A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1473 Processing helix chain 'A' and resid 1489 through 1509 removed outlier: 3.849A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1552 removed outlier: 3.761A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.199A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 removed outlier: 3.666A pdb=" N TYR A1630 " --> pdb=" O PRO A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1650 Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1697 through 1730 removed outlier: 4.067A pdb=" N THR A1703 " --> pdb=" O ASN A1699 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A1704 " --> pdb=" O GLU A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1775 through 1798 Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.704A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1924 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1986 removed outlier: 3.654A pdb=" N HIS A1985 " --> pdb=" O ALA A1981 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A1986 " --> pdb=" O LEU A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 1995 removed outlier: 3.890A pdb=" N ALA A1995 " --> pdb=" O LYS A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 4.279A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2056 Processing helix chain 'A' and resid 2061 through 2080 removed outlier: 3.515A pdb=" N VAL A2070 " --> pdb=" O ALA A2066 " (cutoff:3.500A) Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2131 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 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 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2230 through 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.864A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2320 removed outlier: 4.025A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2359 Processing helix chain 'A' and resid 2365 through 2369 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2410 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 2443 Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.534A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) 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 removed outlier: 3.874A pdb=" N VAL A2552 " --> pdb=" O GLN A2549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2549 through 2552' Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.695A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.534A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.407A 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 2739 through 2757 removed outlier: 4.158A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A2757 " --> pdb=" O ARG A2753 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.741A 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 2903 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 3001 through 3015 removed outlier: 3.929A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (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 Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3221 Processing helix chain 'A' and resid 3471 through 3502 Processing helix chain 'A' and resid 3502 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3580 Processing helix chain 'A' and resid 3594 through 3605 removed outlier: 3.831A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3608 No H-bonds generated for 'chain 'A' and resid 3606 through 3608' Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.502A 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 3651 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3735 removed outlier: 4.280A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3756 Processing helix chain 'A' and resid 3758 through 3763 removed outlier: 3.940A pdb=" N ASP A3762 " --> pdb=" O GLY A3758 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A3763 " --> pdb=" O ARG A3759 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3758 through 3763' Processing helix chain 'A' and resid 3765 through 3786 removed outlier: 3.888A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3818 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 Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.782A pdb=" N ARG A3873 " --> pdb=" O ASN A3869 " (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 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3940 removed outlier: 3.954A pdb=" N CYS A3940 " --> pdb=" O VAL A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3941 through 3945 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.709A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.147A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4013 Processing helix chain 'A' and resid 4014 through 4017 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.814A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4033 Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.937A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4075 through 4091 removed outlier: 4.580A 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 Processing helix chain 'A' and resid 4135 through 4141 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.095A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.732A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4287 through 4291 removed outlier: 3.833A pdb=" N GLY A4290 " --> pdb=" O LYS A4287 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4325 through 4353 removed outlier: 4.061A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A4349 " --> pdb=" O LYS A4345 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A4353 " --> pdb=" O LEU A4349 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.330A 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 4501 through 4506 removed outlier: 3.578A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) 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 4639 Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.382A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.210A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2251 removed outlier: 6.672A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) 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 Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 4.064A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.546A pdb=" N SER A2874 " --> pdb=" O ILE A2882 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.681A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.350A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.280A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.510A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.243A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 4539 through 4543 Processing sheet with id=AC2, first strand: chain 'A' and resid 4583 through 4585 removed outlier: 4.193A pdb=" N LEU A4563 " --> pdb=" O LEU A4585 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 4568 through 4571 1455 hydrogen bonds defined for protein. 4254 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: 13.73 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8067 1.34 - 1.46: 5402 1.46 - 1.58: 11316 1.58 - 1.70: 8 1.70 - 1.82: 206 Bond restraints: 24999 Sorted by residual: bond pdb=" N ILE A1571 " pdb=" CA ILE A1571 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.67e+00 bond pdb=" N ILE A1611 " pdb=" CA ILE A1611 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.45e+00 bond pdb=" N ASP A1606 " pdb=" CA ASP A1606 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.19e-02 7.06e+03 6.03e+00 bond pdb=" N PHE A1551 " pdb=" CA PHE A1551 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.85e+00 bond pdb=" N GLU A1564 " pdb=" CA GLU A1564 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.78e+00 ... (remaining 24994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 33342 2.50 - 5.01: 447 5.01 - 7.51: 75 7.51 - 10.02: 23 10.02 - 12.52: 8 Bond angle restraints: 33895 Sorted by residual: angle pdb=" C ALA A1862 " pdb=" CA ALA A1862 " pdb=" CB ALA A1862 " ideal model delta sigma weight residual 116.63 110.68 5.95 1.16e+00 7.43e-01 2.63e+01 angle pdb=" CA LYS A1580 " pdb=" CB LYS A1580 " pdb=" CG LYS A1580 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CB MET A4247 " pdb=" CG MET A4247 " pdb=" SD MET A4247 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CB MET A2615 " pdb=" CG MET A2615 " pdb=" SD MET A2615 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CA ALA A1862 " pdb=" C ALA A1862 " pdb=" N ASN A1863 " ideal model delta sigma weight residual 119.63 116.71 2.92 8.10e-01 1.52e+00 1.30e+01 ... (remaining 33890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.19: 13693 23.19 - 46.38: 1273 46.38 - 69.58: 167 69.58 - 92.77: 38 92.77 - 115.96: 1 Dihedral angle restraints: 15172 sinusoidal: 6299 harmonic: 8873 Sorted by residual: dihedral pdb=" C5' ADP A4702 " pdb=" O5' ADP A4702 " pdb=" PA ADP A4702 " pdb=" O2A ADP A4702 " ideal model delta sinusoidal sigma weight residual -60.00 55.96 -115.96 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" CA MET A2012 " pdb=" C MET A2012 " pdb=" N ALA A2013 " pdb=" CA ALA A2013 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLU A2839 " pdb=" C GLU A2839 " pdb=" N ASP A2840 " pdb=" CA ASP A2840 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 15169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3726 0.110 - 0.220: 73 0.220 - 0.329: 6 0.329 - 0.439: 0 0.439 - 0.549: 1 Chirality restraints: 3806 Sorted by residual: chirality pdb=" CG LEU A2581 " pdb=" CB LEU A2581 " pdb=" CD1 LEU A2581 " pdb=" CD2 LEU A2581 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" CG LEU A2210 " pdb=" CB LEU A2210 " pdb=" CD1 LEU A2210 " pdb=" CD2 LEU A2210 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU A3479 " pdb=" CB LEU A3479 " pdb=" CD1 LEU A3479 " pdb=" CD2 LEU A3479 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 3803 not shown) Planarity restraints: 4343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1603 " -0.432 9.50e-02 1.11e+02 1.94e-01 2.30e+01 pdb=" NE ARG A1603 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A1603 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1603 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1603 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A4117 " -0.042 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A4118 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A4118 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A4118 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1550 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C ILE A1550 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE A1550 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A1551 " 0.013 2.00e-02 2.50e+03 ... (remaining 4340 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 191 2.51 - 3.11: 19187 3.11 - 3.71: 41281 3.71 - 4.30: 55069 4.30 - 4.90: 90615 Nonbonded interactions: 206343 Sorted by model distance: nonbonded pdb=" O1B ATP A4701 " pdb="MG MG A4704 " model vdw 1.914 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4704 " model vdw 1.947 2.170 nonbonded pdb=" OG SER A1835 " pdb=" OE1 GLU A1837 " model vdw 2.113 3.040 nonbonded pdb=" OH TYR A4180 " pdb=" OD2 ASP A4220 " model vdw 2.122 3.040 nonbonded pdb=" OD1 ASN A2377 " pdb=" O2' ATP A4701 " model vdw 2.123 3.040 ... (remaining 206338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 57.960 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 0.065 24999 Z= 0.178 Angle : 0.755 12.519 33895 Z= 0.388 Chirality : 0.045 0.549 3806 Planarity : 0.005 0.194 4343 Dihedral : 16.966 115.958 9406 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.45 % Allowed : 24.37 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.15), residues: 3019 helix: 1.62 (0.12), residues: 1776 sheet: -1.15 (0.36), residues: 206 loop : 0.19 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A3532 HIS 0.008 0.001 HIS A2918 PHE 0.019 0.001 PHE A3957 TYR 0.037 0.001 TYR A2674 ARG 0.007 0.001 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.12543 ( 1455) hydrogen bonds : angle 5.68544 ( 4254) covalent geometry : bond 0.00354 (24999) covalent geometry : angle 0.75452 (33895) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 272 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8872 (ttp-170) cc_final: 0.8289 (tpt170) REVERT: A 1657 MET cc_start: 0.7962 (mmm) cc_final: 0.7598 (tpt) REVERT: A 2012 MET cc_start: 0.8599 (tpp) cc_final: 0.8360 (mmt) REVERT: A 2145 MET cc_start: 0.8889 (tpt) cc_final: 0.8620 (mmm) REVERT: A 2350 TYR cc_start: 0.8561 (m-80) cc_final: 0.8250 (m-80) REVERT: A 2461 MET cc_start: 0.8858 (mtt) cc_final: 0.8559 (mtt) REVERT: A 3933 GLU cc_start: 0.8912 (pt0) cc_final: 0.8234 (pt0) REVERT: A 4377 MET cc_start: 0.7295 (tpt) cc_final: 0.7065 (tpt) outliers start: 12 outliers final: 8 residues processed: 279 average time/residue: 0.3364 time to fit residues: 153.5737 Evaluate side-chains 252 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 244 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 3125 TYR Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4161 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 274 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2005 GLN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3602 ASN A3792 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.071474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056038 restraints weight = 115729.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.057703 restraints weight = 62233.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058803 restraints weight = 41235.423| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24999 Z= 0.154 Angle : 0.628 10.492 33895 Z= 0.312 Chirality : 0.041 0.300 3806 Planarity : 0.004 0.059 4343 Dihedral : 5.497 112.882 3361 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.34 % Allowed : 20.88 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.15), residues: 3019 helix: 1.95 (0.12), residues: 1798 sheet: -1.00 (0.37), residues: 191 loop : 0.23 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1435 HIS 0.007 0.001 HIS A2918 PHE 0.021 0.001 PHE A3957 TYR 0.024 0.001 TYR A1393 ARG 0.004 0.000 ARG A3174 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 1455) hydrogen bonds : angle 4.62313 ( 4254) covalent geometry : bond 0.00333 (24999) covalent geometry : angle 0.62835 (33895) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8738 (ttp-170) cc_final: 0.8282 (tpt170) REVERT: A 1589 MET cc_start: 0.9174 (mmm) cc_final: 0.8512 (mtp) REVERT: A 1602 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: A 1657 MET cc_start: 0.8026 (mmm) cc_final: 0.7413 (tpt) REVERT: A 1769 MET cc_start: 0.6820 (mmp) cc_final: 0.6609 (mmt) REVERT: A 1820 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8931 (t0) REVERT: A 2012 MET cc_start: 0.8943 (tpp) cc_final: 0.8513 (mmt) REVERT: A 2145 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8787 (mmm) REVERT: A 2461 MET cc_start: 0.9074 (mtt) cc_final: 0.8579 (mtt) REVERT: A 2799 MET cc_start: 0.8320 (ttm) cc_final: 0.8112 (ttt) REVERT: A 2902 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7849 (mm-30) REVERT: A 3006 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: A 3073 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8463 (tm-30) REVERT: A 3077 ASP cc_start: 0.9211 (m-30) cc_final: 0.8905 (m-30) REVERT: A 3181 ASN cc_start: 0.8819 (t0) cc_final: 0.8331 (t0) REVERT: A 3521 ASP cc_start: 0.8706 (p0) cc_final: 0.8394 (p0) REVERT: A 3793 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: A 3819 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8995 (pttp) REVERT: A 3933 GLU cc_start: 0.8953 (pt0) cc_final: 0.8359 (pt0) REVERT: A 4004 MET cc_start: 0.8416 (tmm) cc_final: 0.8026 (tmm) REVERT: A 4030 ILE cc_start: 0.9116 (mm) cc_final: 0.8868 (mm) REVERT: A 4043 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7811 (mpp) REVERT: A 4346 MET cc_start: 0.9155 (mmm) cc_final: 0.8856 (mmp) REVERT: A 4377 MET cc_start: 0.7661 (tpt) cc_final: 0.7107 (mtm) outliers start: 63 outliers final: 23 residues processed: 311 average time/residue: 0.3466 time to fit residues: 177.1411 Evaluate side-chains 269 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1525 ASP Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2707 GLN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3793 GLU Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 106 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054262 restraints weight = 116845.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055873 restraints weight = 63953.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056923 restraints weight = 42674.401| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24999 Z= 0.173 Angle : 0.611 9.556 33895 Z= 0.306 Chirality : 0.041 0.348 3806 Planarity : 0.004 0.050 4343 Dihedral : 5.147 109.241 3352 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.89 % Allowed : 20.59 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.16), residues: 3019 helix: 2.06 (0.12), residues: 1795 sheet: -0.87 (0.36), residues: 199 loop : 0.27 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1435 HIS 0.008 0.001 HIS A2918 PHE 0.014 0.001 PHE A1836 TYR 0.021 0.001 TYR A2748 ARG 0.010 0.000 ARG A2981 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 1455) hydrogen bonds : angle 4.49697 ( 4254) covalent geometry : bond 0.00377 (24999) covalent geometry : angle 0.61131 (33895) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 260 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8786 (ttp-170) cc_final: 0.8309 (tpt170) REVERT: A 1589 MET cc_start: 0.9144 (mmm) cc_final: 0.8376 (mtp) REVERT: A 1602 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: A 1769 MET cc_start: 0.6685 (mmp) cc_final: 0.6409 (mmt) REVERT: A 1820 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8922 (t0) REVERT: A 2041 MET cc_start: 0.8590 (mmm) cc_final: 0.7975 (mmm) REVERT: A 2054 LEU cc_start: 0.9314 (mt) cc_final: 0.9035 (mt) REVERT: A 2087 ASP cc_start: 0.8025 (t0) cc_final: 0.7467 (p0) REVERT: A 2145 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8740 (mmm) REVERT: A 2176 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9148 (t) REVERT: A 2342 MET cc_start: 0.8472 (ptp) cc_final: 0.7993 (ptp) REVERT: A 2461 MET cc_start: 0.9056 (mtt) cc_final: 0.8626 (mtt) REVERT: A 3006 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: A 3073 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 3077 ASP cc_start: 0.9282 (m-30) cc_final: 0.8709 (m-30) REVERT: A 3169 MET cc_start: 0.6567 (mmm) cc_final: 0.5952 (mmm) REVERT: A 3181 ASN cc_start: 0.8926 (t0) cc_final: 0.8393 (t0) REVERT: A 3193 GLU cc_start: 0.9407 (pp20) cc_final: 0.9119 (pp20) REVERT: A 3590 ILE cc_start: 0.8993 (mt) cc_final: 0.8716 (mm) REVERT: A 3749 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7328 (tp) REVERT: A 3791 MET cc_start: 0.8998 (mmp) cc_final: 0.8775 (mmm) REVERT: A 3819 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9040 (pttp) REVERT: A 3933 GLU cc_start: 0.9082 (pt0) cc_final: 0.8519 (pt0) REVERT: A 4002 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8910 (mt) REVERT: A 4004 MET cc_start: 0.8509 (tmm) cc_final: 0.8083 (tmm) REVERT: A 4030 ILE cc_start: 0.8871 (mm) cc_final: 0.8598 (mm) REVERT: A 4043 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: A 4377 MET cc_start: 0.7678 (tpt) cc_final: 0.7100 (mtm) outliers start: 78 outliers final: 37 residues processed: 314 average time/residue: 0.3316 time to fit residues: 171.7433 Evaluate side-chains 276 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1525 ASP Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2707 GLN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 222 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 178 optimal weight: 0.2980 chunk 104 optimal weight: 0.9990 chunk 203 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1397 ASN ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2554 GLN A2689 HIS ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2964 HIS A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3636 GLN A3792 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055692 restraints weight = 117409.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057335 restraints weight = 63501.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058421 restraints weight = 42343.727| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24999 Z= 0.114 Angle : 0.584 11.704 33895 Z= 0.286 Chirality : 0.041 0.462 3806 Planarity : 0.004 0.046 4343 Dihedral : 4.893 99.948 3350 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.52 % Allowed : 21.44 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.16), residues: 3019 helix: 2.14 (0.12), residues: 1791 sheet: -0.96 (0.35), residues: 209 loop : 0.28 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1435 HIS 0.005 0.001 HIS A2918 PHE 0.012 0.001 PHE A3094 TYR 0.019 0.001 TYR A2748 ARG 0.006 0.000 ARG A3611 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 1455) hydrogen bonds : angle 4.29451 ( 4254) covalent geometry : bond 0.00249 (24999) covalent geometry : angle 0.58445 (33895) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 270 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8842 (ttp-170) cc_final: 0.8396 (tpt170) REVERT: A 1500 HIS cc_start: 0.8677 (m90) cc_final: 0.8448 (m90) REVERT: A 1589 MET cc_start: 0.9104 (mmm) cc_final: 0.8380 (mtp) REVERT: A 1602 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: A 1657 MET cc_start: 0.8785 (mmm) cc_final: 0.8175 (tpt) REVERT: A 1820 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8927 (t0) REVERT: A 2041 MET cc_start: 0.8589 (mmm) cc_final: 0.7955 (mmm) REVERT: A 2053 MET cc_start: 0.8400 (ttt) cc_final: 0.7721 (tpt) REVERT: A 2054 LEU cc_start: 0.9209 (mt) cc_final: 0.8855 (mt) REVERT: A 2087 ASP cc_start: 0.7923 (t0) cc_final: 0.7486 (p0) REVERT: A 2131 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8886 (mt) REVERT: A 2145 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8684 (mmm) REVERT: A 2222 MET cc_start: 0.9057 (mmm) cc_final: 0.8778 (mmm) REVERT: A 2342 MET cc_start: 0.8490 (ptp) cc_final: 0.8000 (ptp) REVERT: A 2361 MET cc_start: 0.9029 (ttm) cc_final: 0.8827 (ttm) REVERT: A 2461 MET cc_start: 0.8984 (mtt) cc_final: 0.8583 (mtt) REVERT: A 2773 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8805 (tpp) REVERT: A 3006 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: A 3169 MET cc_start: 0.6646 (mmm) cc_final: 0.6058 (mmm) REVERT: A 3181 ASN cc_start: 0.8899 (t0) cc_final: 0.8291 (t0) REVERT: A 3590 ILE cc_start: 0.8965 (mt) cc_final: 0.8715 (mm) REVERT: A 3601 MET cc_start: 0.8996 (mpp) cc_final: 0.8062 (mpp) REVERT: A 3695 ARG cc_start: 0.8980 (mtt90) cc_final: 0.8770 (mpp80) REVERT: A 3749 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7470 (tp) REVERT: A 3786 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8550 (pt0) REVERT: A 3791 MET cc_start: 0.9144 (mmp) cc_final: 0.8943 (mmm) REVERT: A 3819 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9031 (pttp) REVERT: A 3933 GLU cc_start: 0.9055 (pt0) cc_final: 0.8496 (pt0) REVERT: A 4002 LEU cc_start: 0.9114 (tt) cc_final: 0.8855 (mt) REVERT: A 4030 ILE cc_start: 0.8822 (mm) cc_final: 0.8553 (mm) REVERT: A 4043 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7855 (mpp) REVERT: A 4095 MET cc_start: 0.6826 (tpp) cc_final: 0.6197 (tpp) REVERT: A 4311 LEU cc_start: 0.9343 (pp) cc_final: 0.8934 (mm) outliers start: 68 outliers final: 34 residues processed: 312 average time/residue: 0.3290 time to fit residues: 168.0216 Evaluate side-chains 284 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1525 ASP Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2707 GLN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2773 MET Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2926 PHE Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3062 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 276 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 202 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 ASN ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.051842 restraints weight = 119941.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053375 restraints weight = 65170.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054383 restraints weight = 43712.588| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24999 Z= 0.250 Angle : 0.668 11.507 33895 Z= 0.335 Chirality : 0.043 0.454 3806 Planarity : 0.004 0.050 4343 Dihedral : 5.087 104.262 3350 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.60 % Allowed : 20.99 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.16), residues: 3019 helix: 2.04 (0.12), residues: 1788 sheet: -1.14 (0.37), residues: 192 loop : 0.27 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1435 HIS 0.006 0.001 HIS A1412 PHE 0.025 0.002 PHE A3513 TYR 0.015 0.002 TYR A3812 ARG 0.007 0.001 ARG A2726 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 1455) hydrogen bonds : angle 4.55825 ( 4254) covalent geometry : bond 0.00541 (24999) covalent geometry : angle 0.66825 (33895) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 225 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8865 (ttp-170) cc_final: 0.8358 (tpt170) REVERT: A 1589 MET cc_start: 0.9104 (mmm) cc_final: 0.8378 (mtp) REVERT: A 1602 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: A 1733 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6175 (mp) REVERT: A 1820 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8620 (t0) REVERT: A 2041 MET cc_start: 0.8700 (mmm) cc_final: 0.8090 (mmm) REVERT: A 2054 LEU cc_start: 0.9428 (mt) cc_final: 0.9155 (mt) REVERT: A 2087 ASP cc_start: 0.8065 (t0) cc_final: 0.7501 (p0) REVERT: A 2131 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9001 (mt) REVERT: A 2145 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8681 (mmm) REVERT: A 2176 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9130 (t) REVERT: A 2222 MET cc_start: 0.9261 (mmm) cc_final: 0.8918 (mmm) REVERT: A 2361 MET cc_start: 0.9125 (ttm) cc_final: 0.8847 (ttm) REVERT: A 2692 PHE cc_start: 0.8808 (p90) cc_final: 0.8514 (p90) REVERT: A 2965 ARG cc_start: 0.8339 (mtp85) cc_final: 0.8025 (mtp85) REVERT: A 3006 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: A 3073 GLU cc_start: 0.9023 (pp20) cc_final: 0.8516 (tm-30) REVERT: A 3077 ASP cc_start: 0.9345 (m-30) cc_final: 0.8895 (m-30) REVERT: A 3169 MET cc_start: 0.7005 (mmm) cc_final: 0.6415 (mmm) REVERT: A 3590 ILE cc_start: 0.9111 (mt) cc_final: 0.8862 (mm) REVERT: A 3601 MET cc_start: 0.8989 (mpp) cc_final: 0.8214 (mpp) REVERT: A 3819 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9128 (pttp) REVERT: A 3933 GLU cc_start: 0.9174 (pt0) cc_final: 0.8685 (pt0) REVERT: A 4002 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8952 (mt) REVERT: A 4030 ILE cc_start: 0.8978 (mm) cc_final: 0.8713 (mm) REVERT: A 4043 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8020 (mpp) REVERT: A 4095 MET cc_start: 0.7294 (tpp) cc_final: 0.6662 (tpp) REVERT: A 4377 MET cc_start: 0.7791 (tpt) cc_final: 0.7319 (mtm) outliers start: 97 outliers final: 53 residues processed: 299 average time/residue: 0.3197 time to fit residues: 159.1572 Evaluate side-chains 276 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1525 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2339 VAL Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2660 VAL Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2707 GLN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3863 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 3992 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 233 optimal weight: 5.9990 chunk 290 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2857 HIS A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.067380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.052229 restraints weight = 118806.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053789 restraints weight = 64231.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054797 restraints weight = 43057.494| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24999 Z= 0.171 Angle : 0.623 15.195 33895 Z= 0.306 Chirality : 0.042 0.497 3806 Planarity : 0.004 0.047 4343 Dihedral : 5.017 98.645 3350 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.93 % Allowed : 21.66 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.16), residues: 3019 helix: 2.07 (0.12), residues: 1791 sheet: -1.08 (0.35), residues: 218 loop : 0.27 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1435 HIS 0.007 0.001 HIS A2918 PHE 0.018 0.001 PHE A3094 TYR 0.026 0.001 TYR A2674 ARG 0.006 0.000 ARG A3611 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 1455) hydrogen bonds : angle 4.40114 ( 4254) covalent geometry : bond 0.00375 (24999) covalent geometry : angle 0.62266 (33895) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 235 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8902 (ttp-170) cc_final: 0.8353 (tpt170) REVERT: A 1589 MET cc_start: 0.9114 (mmm) cc_final: 0.8419 (mtp) REVERT: A 1602 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: A 1657 MET cc_start: 0.8944 (mmm) cc_final: 0.8701 (mmm) REVERT: A 1820 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8662 (t0) REVERT: A 2000 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8614 (tp30) REVERT: A 2012 MET cc_start: 0.8926 (mmt) cc_final: 0.8706 (mmm) REVERT: A 2041 MET cc_start: 0.8689 (mmm) cc_final: 0.8049 (mmm) REVERT: A 2053 MET cc_start: 0.8534 (ttt) cc_final: 0.7911 (tpt) REVERT: A 2054 LEU cc_start: 0.9349 (mt) cc_final: 0.8989 (mt) REVERT: A 2087 ASP cc_start: 0.7827 (t0) cc_final: 0.7374 (p0) REVERT: A 2145 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8670 (mmm) REVERT: A 2222 MET cc_start: 0.9269 (mmm) cc_final: 0.8894 (mmm) REVERT: A 2361 MET cc_start: 0.9103 (ttm) cc_final: 0.8852 (ttm) REVERT: A 2461 MET cc_start: 0.9083 (mtt) cc_final: 0.8717 (mtt) REVERT: A 2692 PHE cc_start: 0.8819 (p90) cc_final: 0.8529 (p90) REVERT: A 2773 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8874 (tpp) REVERT: A 2898 LYS cc_start: 0.8987 (tppt) cc_final: 0.8602 (tppt) REVERT: A 2902 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: A 2965 ARG cc_start: 0.8367 (mtp85) cc_final: 0.8018 (mtp85) REVERT: A 3006 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: A 3073 GLU cc_start: 0.8986 (pp20) cc_final: 0.8515 (pp20) REVERT: A 3077 ASP cc_start: 0.9339 (m-30) cc_final: 0.9002 (m-30) REVERT: A 3195 GLU cc_start: 0.9335 (tm-30) cc_final: 0.9104 (mp0) REVERT: A 3601 MET cc_start: 0.9142 (mpp) cc_final: 0.8183 (mpp) REVERT: A 3815 MET cc_start: 0.9437 (mtp) cc_final: 0.9105 (mtm) REVERT: A 3819 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9122 (pttp) REVERT: A 3933 GLU cc_start: 0.9159 (pt0) cc_final: 0.8690 (pt0) REVERT: A 4002 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9011 (mt) REVERT: A 4030 ILE cc_start: 0.8951 (mm) cc_final: 0.8682 (mm) REVERT: A 4095 MET cc_start: 0.7333 (tpp) cc_final: 0.6704 (tpp) REVERT: A 4311 LEU cc_start: 0.9330 (pp) cc_final: 0.8940 (mm) REVERT: A 4377 MET cc_start: 0.7645 (tpt) cc_final: 0.7227 (mtm) outliers start: 79 outliers final: 55 residues processed: 292 average time/residue: 0.3380 time to fit residues: 162.5801 Evaluate side-chains 281 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1525 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 1974 GLN Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2660 VAL Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2707 GLN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2773 MET Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3617 ASP Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3763 ASP Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4541 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 287 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 290 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 281 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 256 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2485 GLN ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS A3198 GLN ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.067173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052062 restraints weight = 119224.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053619 restraints weight = 64208.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054650 restraints weight = 42932.312| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24999 Z= 0.155 Angle : 0.619 11.599 33895 Z= 0.303 Chirality : 0.042 0.495 3806 Planarity : 0.004 0.055 4343 Dihedral : 4.987 96.574 3350 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.30 % Allowed : 21.03 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.16), residues: 3019 helix: 2.08 (0.12), residues: 1791 sheet: -1.07 (0.35), residues: 218 loop : 0.28 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1435 HIS 0.006 0.001 HIS A2918 PHE 0.034 0.001 PHE A3513 TYR 0.032 0.001 TYR A2674 ARG 0.004 0.000 ARG A2869 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 1455) hydrogen bonds : angle 4.34083 ( 4254) covalent geometry : bond 0.00343 (24999) covalent geometry : angle 0.61932 (33895) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 230 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8887 (ttp-170) cc_final: 0.8464 (tpt170) REVERT: A 1589 MET cc_start: 0.9082 (mmm) cc_final: 0.8354 (mtp) REVERT: A 1602 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: A 1820 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8727 (t0) REVERT: A 2012 MET cc_start: 0.8883 (mmt) cc_final: 0.8552 (mmm) REVERT: A 2041 MET cc_start: 0.8714 (mmm) cc_final: 0.8071 (mmm) REVERT: A 2053 MET cc_start: 0.8458 (ttt) cc_final: 0.7902 (tpt) REVERT: A 2054 LEU cc_start: 0.9355 (mt) cc_final: 0.8980 (mt) REVERT: A 2087 ASP cc_start: 0.7604 (t0) cc_final: 0.7142 (p0) REVERT: A 2145 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8689 (mmm) REVERT: A 2149 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9156 (tp) REVERT: A 2176 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9086 (t) REVERT: A 2222 MET cc_start: 0.9240 (mmm) cc_final: 0.8902 (mmm) REVERT: A 2361 MET cc_start: 0.9039 (ttm) cc_final: 0.8785 (ttm) REVERT: A 2461 MET cc_start: 0.9085 (mtt) cc_final: 0.8740 (mtt) REVERT: A 2692 PHE cc_start: 0.8831 (p90) cc_final: 0.8535 (p90) REVERT: A 2965 ARG cc_start: 0.8387 (mtp85) cc_final: 0.8015 (mtp85) REVERT: A 3006 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: A 3073 GLU cc_start: 0.8984 (pp20) cc_final: 0.8639 (pp20) REVERT: A 3077 ASP cc_start: 0.9325 (m-30) cc_final: 0.8997 (m-30) REVERT: A 3195 GLU cc_start: 0.9367 (tm-30) cc_final: 0.9093 (mp0) REVERT: A 3601 MET cc_start: 0.9222 (mpp) cc_final: 0.8358 (mpp) REVERT: A 3786 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8437 (pt0) REVERT: A 3815 MET cc_start: 0.9423 (mtp) cc_final: 0.9102 (mtm) REVERT: A 3819 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9121 (pttp) REVERT: A 3933 GLU cc_start: 0.9192 (pt0) cc_final: 0.8740 (pt0) REVERT: A 3946 ASP cc_start: 0.8373 (p0) cc_final: 0.7927 (t0) REVERT: A 4002 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9066 (mt) REVERT: A 4030 ILE cc_start: 0.8979 (mm) cc_final: 0.8728 (mm) REVERT: A 4082 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8770 (mmtm) REVERT: A 4095 MET cc_start: 0.7432 (tpp) cc_final: 0.6834 (tpp) REVERT: A 4128 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7807 (ppp) REVERT: A 4311 LEU cc_start: 0.9329 (pp) cc_final: 0.8941 (mm) REVERT: A 4377 MET cc_start: 0.7517 (tpt) cc_final: 0.7085 (mtm) outliers start: 89 outliers final: 60 residues processed: 295 average time/residue: 0.3377 time to fit residues: 163.0049 Evaluate side-chains 289 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 220 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1495 ASN Chi-restraints excluded: chain A residue 1525 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 1974 GLN Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2339 VAL Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2660 VAL Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2707 GLN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2752 ASN Chi-restraints excluded: chain A residue 2773 MET Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3617 ASP Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3763 ASP Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 3992 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4541 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 144 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 272 optimal weight: 0.0570 chunk 234 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3792 GLN A4029 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.068072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052960 restraints weight = 117639.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054531 restraints weight = 63568.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.055560 restraints weight = 42480.556| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24999 Z= 0.122 Angle : 0.623 16.080 33895 Z= 0.299 Chirality : 0.041 0.508 3806 Planarity : 0.004 0.048 4343 Dihedral : 4.883 91.663 3350 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.82 % Allowed : 22.22 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.16), residues: 3019 helix: 2.12 (0.12), residues: 1790 sheet: -0.99 (0.35), residues: 219 loop : 0.33 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1435 HIS 0.006 0.001 HIS A2918 PHE 0.016 0.001 PHE A3094 TYR 0.026 0.001 TYR A2674 ARG 0.007 0.000 ARG A1485 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 1455) hydrogen bonds : angle 4.28191 ( 4254) covalent geometry : bond 0.00271 (24999) covalent geometry : angle 0.62340 (33895) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 236 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8897 (ttp-170) cc_final: 0.8464 (tpt-90) REVERT: A 1589 MET cc_start: 0.9085 (mmm) cc_final: 0.8349 (mtp) REVERT: A 1820 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8728 (t0) REVERT: A 2000 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8588 (tp30) REVERT: A 2012 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8373 (mmm) REVERT: A 2039 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8504 (tp) REVERT: A 2053 MET cc_start: 0.8417 (ttt) cc_final: 0.7860 (tpt) REVERT: A 2054 LEU cc_start: 0.9315 (mt) cc_final: 0.8922 (mt) REVERT: A 2087 ASP cc_start: 0.7475 (t0) cc_final: 0.7094 (p0) REVERT: A 2145 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8637 (mmm) REVERT: A 2176 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9059 (t) REVERT: A 2222 MET cc_start: 0.9118 (mmm) cc_final: 0.8870 (mmm) REVERT: A 2361 MET cc_start: 0.8999 (ttm) cc_final: 0.8754 (ttm) REVERT: A 2373 MET cc_start: 0.8666 (ptp) cc_final: 0.8409 (ptp) REVERT: A 2461 MET cc_start: 0.8996 (mtt) cc_final: 0.8621 (mtt) REVERT: A 2692 PHE cc_start: 0.8744 (p90) cc_final: 0.8456 (p90) REVERT: A 2965 ARG cc_start: 0.8334 (mtp85) cc_final: 0.7976 (mtp85) REVERT: A 3006 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: A 3073 GLU cc_start: 0.8963 (pp20) cc_final: 0.8598 (pp20) REVERT: A 3077 ASP cc_start: 0.9300 (m-30) cc_final: 0.8951 (m-30) REVERT: A 3169 MET cc_start: 0.6787 (mmm) cc_final: 0.6410 (mmm) REVERT: A 3195 GLU cc_start: 0.9248 (tm-30) cc_final: 0.9045 (mp0) REVERT: A 3601 MET cc_start: 0.9155 (mpp) cc_final: 0.8255 (mpp) REVERT: A 3786 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8416 (pt0) REVERT: A 3815 MET cc_start: 0.9392 (mtp) cc_final: 0.9134 (mtm) REVERT: A 3819 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9100 (pttp) REVERT: A 3933 GLU cc_start: 0.9178 (pt0) cc_final: 0.8729 (pt0) REVERT: A 3946 ASP cc_start: 0.8254 (p0) cc_final: 0.7922 (t0) REVERT: A 4004 MET cc_start: 0.8484 (ppp) cc_final: 0.8239 (tmm) REVERT: A 4030 ILE cc_start: 0.8953 (mm) cc_final: 0.8699 (mm) REVERT: A 4095 MET cc_start: 0.7372 (tpp) cc_final: 0.6830 (tpp) REVERT: A 4128 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7822 (ppp) REVERT: A 4311 LEU cc_start: 0.9325 (pp) cc_final: 0.8931 (mm) REVERT: A 4377 MET cc_start: 0.7525 (tpt) cc_final: 0.7092 (mtm) outliers start: 76 outliers final: 51 residues processed: 291 average time/residue: 0.3475 time to fit residues: 165.3833 Evaluate side-chains 281 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1525 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 1974 GLN Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2752 ASN Chi-restraints excluded: chain A residue 2773 MET Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3617 ASP Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3767 ILE Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4468 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 70 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 257 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 225 optimal weight: 0.0970 chunk 106 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS A3499 GLN ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3650 ASN ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.067198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052245 restraints weight = 118245.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.053798 restraints weight = 63589.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054816 restraints weight = 42439.220| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24999 Z= 0.145 Angle : 0.643 14.454 33895 Z= 0.308 Chirality : 0.042 0.495 3806 Planarity : 0.004 0.054 4343 Dihedral : 4.877 92.904 3350 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.52 % Allowed : 22.70 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.16), residues: 3019 helix: 2.08 (0.12), residues: 1790 sheet: -1.06 (0.34), residues: 219 loop : 0.33 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1435 HIS 0.007 0.001 HIS A2918 PHE 0.038 0.001 PHE A3513 TYR 0.024 0.001 TYR A2674 ARG 0.009 0.000 ARG A3695 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 1455) hydrogen bonds : angle 4.32098 ( 4254) covalent geometry : bond 0.00323 (24999) covalent geometry : angle 0.64294 (33895) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 227 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8905 (ttp-170) cc_final: 0.8474 (tpt-90) REVERT: A 1589 MET cc_start: 0.9087 (mmm) cc_final: 0.8399 (mtp) REVERT: A 1602 GLU cc_start: 0.8196 (mp0) cc_final: 0.7834 (mp0) REVERT: A 1657 MET cc_start: 0.8968 (mmm) cc_final: 0.8549 (tpt) REVERT: A 1820 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8709 (t0) REVERT: A 2000 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8559 (tp30) REVERT: A 2012 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8493 (mmm) REVERT: A 2053 MET cc_start: 0.8483 (ttt) cc_final: 0.7903 (tpt) REVERT: A 2054 LEU cc_start: 0.9357 (mt) cc_final: 0.8953 (mt) REVERT: A 2087 ASP cc_start: 0.7570 (t0) cc_final: 0.7199 (p0) REVERT: A 2145 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8648 (mmm) REVERT: A 2176 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9054 (t) REVERT: A 2222 MET cc_start: 0.9183 (mmm) cc_final: 0.8886 (mmm) REVERT: A 2304 ASP cc_start: 0.7748 (t0) cc_final: 0.7504 (t0) REVERT: A 2373 MET cc_start: 0.8727 (ptp) cc_final: 0.8436 (ptp) REVERT: A 2461 MET cc_start: 0.9045 (mtt) cc_final: 0.8640 (mtt) REVERT: A 2692 PHE cc_start: 0.8800 (p90) cc_final: 0.8503 (p90) REVERT: A 2799 MET cc_start: 0.8713 (ttt) cc_final: 0.8445 (tpp) REVERT: A 2965 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7974 (mtp85) REVERT: A 3006 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7712 (mm-30) REVERT: A 3073 GLU cc_start: 0.9007 (pp20) cc_final: 0.8736 (pp20) REVERT: A 3077 ASP cc_start: 0.9322 (m-30) cc_final: 0.9098 (m-30) REVERT: A 3169 MET cc_start: 0.6886 (mmm) cc_final: 0.6532 (mmm) REVERT: A 3195 GLU cc_start: 0.9260 (tm-30) cc_final: 0.9037 (mp0) REVERT: A 3601 MET cc_start: 0.9171 (mpp) cc_final: 0.8284 (mpp) REVERT: A 3749 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7774 (tt) REVERT: A 3786 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8438 (pt0) REVERT: A 3815 MET cc_start: 0.9415 (mtp) cc_final: 0.9169 (mtm) REVERT: A 3819 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9115 (pttp) REVERT: A 3933 GLU cc_start: 0.9190 (pt0) cc_final: 0.8769 (pt0) REVERT: A 3946 ASP cc_start: 0.8300 (p0) cc_final: 0.8000 (t0) REVERT: A 4095 MET cc_start: 0.7482 (tpp) cc_final: 0.6962 (tpp) REVERT: A 4128 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7889 (ppp) REVERT: A 4311 LEU cc_start: 0.9303 (pp) cc_final: 0.8879 (mm) REVERT: A 4377 MET cc_start: 0.7547 (tpt) cc_final: 0.7093 (mtm) outliers start: 68 outliers final: 50 residues processed: 279 average time/residue: 0.3337 time to fit residues: 152.6214 Evaluate side-chains 279 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 220 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1525 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 1974 GLN Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2752 ASN Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3617 ASP Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3767 ILE Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 3992 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4468 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 42 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 242 optimal weight: 0.0040 chunk 175 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 290 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3854 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.067660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.052635 restraints weight = 118011.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054247 restraints weight = 62445.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055286 restraints weight = 41130.005| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24999 Z= 0.119 Angle : 0.658 15.381 33895 Z= 0.310 Chirality : 0.042 0.510 3806 Planarity : 0.004 0.047 4343 Dihedral : 4.813 88.200 3350 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.23 % Allowed : 23.22 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.16), residues: 3019 helix: 2.07 (0.12), residues: 1788 sheet: -1.04 (0.34), residues: 219 loop : 0.30 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1435 HIS 0.006 0.001 HIS A2918 PHE 0.018 0.001 PHE A3513 TYR 0.022 0.001 TYR A2674 ARG 0.012 0.000 ARG A3695 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 1455) hydrogen bonds : angle 4.27026 ( 4254) covalent geometry : bond 0.00265 (24999) covalent geometry : angle 0.65756 (33895) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8901 (ttp-170) cc_final: 0.8495 (tpt-90) REVERT: A 1589 MET cc_start: 0.9067 (mmm) cc_final: 0.8228 (mtp) REVERT: A 1602 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 1657 MET cc_start: 0.9016 (mmm) cc_final: 0.8570 (tpt) REVERT: A 1820 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8782 (t0) REVERT: A 2000 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8582 (tp30) REVERT: A 2012 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8558 (mmm) REVERT: A 2053 MET cc_start: 0.8583 (ttt) cc_final: 0.7941 (tpt) REVERT: A 2054 LEU cc_start: 0.9373 (mt) cc_final: 0.8953 (mt) REVERT: A 2087 ASP cc_start: 0.7501 (t0) cc_final: 0.7060 (p0) REVERT: A 2176 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8974 (t) REVERT: A 2222 MET cc_start: 0.9016 (mmm) cc_final: 0.8761 (mmm) REVERT: A 2304 ASP cc_start: 0.7724 (t0) cc_final: 0.7453 (t0) REVERT: A 2373 MET cc_start: 0.8714 (ptp) cc_final: 0.8415 (ptp) REVERT: A 2461 MET cc_start: 0.9060 (mtt) cc_final: 0.8669 (mtt) REVERT: A 2692 PHE cc_start: 0.8909 (p90) cc_final: 0.8606 (p90) REVERT: A 2799 MET cc_start: 0.8765 (ttt) cc_final: 0.8361 (tpp) REVERT: A 2965 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7999 (mtp85) REVERT: A 3006 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7672 (mm-30) REVERT: A 3073 GLU cc_start: 0.9001 (pp20) cc_final: 0.8613 (pp20) REVERT: A 3077 ASP cc_start: 0.9369 (m-30) cc_final: 0.9035 (m-30) REVERT: A 3169 MET cc_start: 0.6881 (mmm) cc_final: 0.6518 (mmm) REVERT: A 3195 GLU cc_start: 0.9236 (tm-30) cc_final: 0.9031 (mp0) REVERT: A 3601 MET cc_start: 0.9167 (mpp) cc_final: 0.8252 (mpp) REVERT: A 3749 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7581 (tp) REVERT: A 3786 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8431 (pt0) REVERT: A 3815 MET cc_start: 0.9412 (mtp) cc_final: 0.9194 (mtm) REVERT: A 3819 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9103 (pttp) REVERT: A 3933 GLU cc_start: 0.9162 (pt0) cc_final: 0.8738 (pt0) REVERT: A 4095 MET cc_start: 0.7578 (tpp) cc_final: 0.7117 (tpp) REVERT: A 4128 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7847 (ppp) REVERT: A 4311 LEU cc_start: 0.9321 (pp) cc_final: 0.8920 (mm) REVERT: A 4377 MET cc_start: 0.7393 (tpt) cc_final: 0.6956 (mtm) outliers start: 60 outliers final: 44 residues processed: 279 average time/residue: 0.3426 time to fit residues: 157.8457 Evaluate side-chains 279 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1525 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1974 GLN Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3189 GLU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3617 ASP Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4468 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 50 optimal weight: 0.6980 chunk 214 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 chunk 263 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1593 ASN ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.067062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052143 restraints weight = 118388.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053732 restraints weight = 62600.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054742 restraints weight = 41246.077| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24999 Z= 0.139 Angle : 0.669 15.417 33895 Z= 0.319 Chirality : 0.042 0.497 3806 Planarity : 0.004 0.048 4343 Dihedral : 4.838 89.718 3349 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.26 % Allowed : 23.41 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.16), residues: 3019 helix: 2.12 (0.12), residues: 1775 sheet: -1.09 (0.33), residues: 229 loop : 0.36 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1435 HIS 0.006 0.001 HIS A2918 PHE 0.017 0.001 PHE A1686 TYR 0.021 0.001 TYR A2748 ARG 0.011 0.000 ARG A3695 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1455) hydrogen bonds : angle 4.28064 ( 4254) covalent geometry : bond 0.00310 (24999) covalent geometry : angle 0.66880 (33895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7506.92 seconds wall clock time: 132 minutes 31.27 seconds (7951.27 seconds total)