Starting phenix.real_space_refine on Fri Sep 19 10:09:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bn1_44718/09_2025/9bn1_44718.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bn1_44718/09_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_44718/09_2025/9bn1_44718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bn1_44718/09_2025/9bn1_44718.map" model { file = "/net/cci-nas-00/data/ceres_data/9bn1_44718/09_2025/9bn1_44718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bn1_44718/09_2025/9bn1_44718.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.57, per 1000 atoms: 0.23 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: 2.26 Conformation dependent library (CDL) restraints added in 961.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.78 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: 7.29 Time building geometry restraints manager: 2.97 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.320 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG A3544 TYR 0.037 0.001 TYR A2674 PHE 0.019 0.001 PHE A3957 TRP 0.020 0.001 TRP A3532 HIS 0.008 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00354 (24999) covalent geometry : angle 0.75452 (33895) hydrogen bonds : bond 0.12543 ( 1455) hydrogen bonds : angle 5.68544 ( 4254) *********************** 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 : 0.981 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: 0.1598 time to fit residues: 73.5558 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 : 1.065 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3175 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.070022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054629 restraints weight = 117852.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.056225 restraints weight = 64190.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.057294 restraints weight = 43075.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057946 restraints weight = 32824.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.058424 restraints weight = 27548.033| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24999 Z= 0.189 Angle : 0.643 9.555 33895 Z= 0.323 Chirality : 0.042 0.303 3806 Planarity : 0.004 0.061 4343 Dihedral : 5.561 114.522 3361 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.82 % Allowed : 20.77 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.15), residues: 3019 helix: 1.91 (0.12), residues: 1796 sheet: -1.04 (0.35), residues: 218 loop : 0.27 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2726 TYR 0.025 0.002 TYR A2748 PHE 0.017 0.001 PHE A1836 TRP 0.024 0.002 TRP A1435 HIS 0.009 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00412 (24999) covalent geometry : angle 0.64326 (33895) hydrogen bonds : bond 0.04412 ( 1455) hydrogen bonds : angle 4.64578 ( 4254) *********************** 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 336 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 260 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8747 (ttp-170) cc_final: 0.8282 (tpt170) REVERT: A 1589 MET cc_start: 0.9189 (mmm) cc_final: 0.8545 (mtp) REVERT: A 1602 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: A 1769 MET cc_start: 0.6464 (mmp) cc_final: 0.6242 (mmt) REVERT: A 1820 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8887 (t0) REVERT: A 2012 MET cc_start: 0.9028 (tpp) cc_final: 0.8781 (tpp) REVERT: A 2041 MET cc_start: 0.8507 (mmm) cc_final: 0.7796 (mmm) REVERT: A 2145 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8753 (mmm) REVERT: A 2461 MET cc_start: 0.9044 (mtt) cc_final: 0.8591 (mtt) REVERT: A 2633 LYS cc_start: 0.9139 (mmtm) cc_final: 0.8906 (mptt) REVERT: A 2799 MET cc_start: 0.8345 (ttm) cc_final: 0.8105 (ttt) REVERT: A 2902 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: A 3006 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7457 (mm-30) REVERT: A 3073 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 3077 ASP cc_start: 0.9101 (m-30) cc_final: 0.8778 (m-30) REVERT: A 3521 ASP cc_start: 0.8603 (p0) cc_final: 0.8307 (p0) REVERT: A 3749 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7152 (tp) REVERT: A 3819 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9035 (pttp) REVERT: A 3933 GLU cc_start: 0.8974 (pt0) cc_final: 0.8421 (pt0) REVERT: A 4004 MET cc_start: 0.8442 (tmm) cc_final: 0.7796 (tmm) REVERT: A 4030 ILE cc_start: 0.9108 (mm) cc_final: 0.8857 (mm) REVERT: A 4043 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7870 (mpp) REVERT: A 4377 MET cc_start: 0.7647 (tpt) cc_final: 0.7202 (mtm) outliers start: 76 outliers final: 30 residues processed: 318 average time/residue: 0.1478 time to fit residues: 77.2644 Evaluate side-chains 268 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 1647 VAL 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 2131 LEU Chi-restraints excluded: chain A residue 2141 VAL 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 2617 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 2963 VAL 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 3749 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 33 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 295 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3636 GLN A3792 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.069474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054222 restraints weight = 117451.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055839 restraints weight = 63639.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056894 restraints weight = 42465.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.057583 restraints weight = 32433.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057993 restraints weight = 27039.209| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1479 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= 0.162 Angle : 0.605 9.431 33895 Z= 0.302 Chirality : 0.041 0.349 3806 Planarity : 0.004 0.051 4343 Dihedral : 5.153 109.511 3352 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.86 % Allowed : 20.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.15), residues: 3019 helix: 2.03 (0.12), residues: 1793 sheet: -1.09 (0.35), residues: 211 loop : 0.24 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3611 TYR 0.021 0.001 TYR A2748 PHE 0.020 0.001 PHE A2682 TRP 0.022 0.001 TRP A1435 HIS 0.007 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00351 (24999) covalent geometry : angle 0.60528 (33895) hydrogen bonds : bond 0.04108 ( 1455) hydrogen bonds : angle 4.47651 ( 4254) *********************** 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 332 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 255 time to evaluate : 0.754 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: 0.8799 (ttp-170) cc_final: 0.8319 (tpt170) REVERT: A 1589 MET cc_start: 0.9138 (mmm) cc_final: 0.8384 (mtp) REVERT: A 1602 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: A 1657 MET cc_start: 0.8727 (mmm) cc_final: 0.8143 (tpt) REVERT: A 1733 ILE cc_start: 0.6494 (OUTLIER) cc_final: 0.6067 (mp) REVERT: A 1769 MET cc_start: 0.6441 (mmp) cc_final: 0.6150 (mmt) REVERT: A 1820 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8904 (t0) REVERT: A 2041 MET cc_start: 0.8583 (mmm) cc_final: 0.7992 (mmm) REVERT: A 2054 LEU cc_start: 0.9339 (mt) cc_final: 0.9065 (mt) REVERT: A 2087 ASP cc_start: 0.8000 (t0) cc_final: 0.7444 (p0) REVERT: A 2145 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8774 (mmm) REVERT: A 2176 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9148 (t) REVERT: A 2342 MET cc_start: 0.8518 (ptp) cc_final: 0.8047 (ptp) REVERT: A 2461 MET cc_start: 0.9038 (mtt) cc_final: 0.8621 (mtt) REVERT: A 3006 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: A 3073 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 3077 ASP cc_start: 0.9214 (m-30) cc_final: 0.8632 (m-30) REVERT: A 3169 MET cc_start: 0.6558 (mmm) cc_final: 0.5938 (mmm) REVERT: A 3181 ASN cc_start: 0.8935 (t0) cc_final: 0.8410 (t0) REVERT: A 3521 ASP cc_start: 0.8441 (p0) cc_final: 0.8212 (p0) REVERT: A 3590 ILE cc_start: 0.8947 (mt) cc_final: 0.8720 (mm) REVERT: A 3601 MET cc_start: 0.9000 (mpp) cc_final: 0.8164 (mpp) REVERT: A 3749 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7442 (tp) REVERT: A 3791 MET cc_start: 0.8909 (mmp) cc_final: 0.8702 (mmp) REVERT: A 3819 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9041 (pttp) REVERT: A 3933 GLU cc_start: 0.9062 (pt0) cc_final: 0.8500 (pt0) REVERT: A 4002 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8887 (mt) REVERT: A 4004 MET cc_start: 0.8456 (tmm) cc_final: 0.8177 (tmm) REVERT: A 4030 ILE cc_start: 0.8874 (mm) cc_final: 0.8591 (mm) REVERT: A 4043 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7885 (mpp) REVERT: A 4346 MET cc_start: 0.9081 (mmm) cc_final: 0.8671 (mmp) REVERT: A 4377 MET cc_start: 0.7530 (tpt) cc_final: 0.7168 (mtm) outliers start: 77 outliers final: 37 residues processed: 307 average time/residue: 0.1412 time to fit residues: 72.1696 Evaluate side-chains 280 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 1637 LEU Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1820 ASP 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 2562 VAL 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 2902 GLU Chi-restraints excluded: chain A residue 2920 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 3122 VAL 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 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4436 GLN 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 161 optimal weight: 0.0570 chunk 147 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 184 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1397 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 ASN A2689 HIS A2752 ASN ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2964 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053642 restraints weight = 117802.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055225 restraints weight = 63777.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056263 restraints weight = 42644.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056882 restraints weight = 32626.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057349 restraints weight = 27550.774| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1932 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= 0.164 Angle : 0.599 12.007 33895 Z= 0.299 Chirality : 0.041 0.431 3806 Planarity : 0.004 0.068 4343 Dihedral : 5.020 104.469 3350 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.41 % Allowed : 20.62 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.16), residues: 3019 helix: 2.10 (0.12), residues: 1788 sheet: -1.09 (0.35), residues: 211 loop : 0.30 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A3611 TYR 0.020 0.001 TYR A2748 PHE 0.015 0.001 PHE A3513 TRP 0.024 0.001 TRP A1435 HIS 0.007 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00362 (24999) covalent geometry : angle 0.59897 (33895) hydrogen bonds : bond 0.03952 ( 1455) hydrogen bonds : angle 4.40140 ( 4254) *********************** 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 334 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 242 time to evaluate : 0.964 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: 0.8838 (ttp-170) cc_final: 0.8372 (tpt170) REVERT: A 1589 MET cc_start: 0.9093 (mmm) cc_final: 0.8377 (mtp) REVERT: A 1602 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: A 1733 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.6196 (mp) REVERT: A 1820 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8606 (t0) REVERT: A 2041 MET cc_start: 0.8674 (mmm) cc_final: 0.8099 (mmm) REVERT: A 2054 LEU cc_start: 0.9387 (mt) cc_final: 0.9105 (mt) REVERT: A 2087 ASP cc_start: 0.7960 (t0) cc_final: 0.7495 (p0) REVERT: A 2131 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8966 (mt) REVERT: A 2145 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8744 (mmm) REVERT: A 2176 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9116 (t) REVERT: A 2342 MET cc_start: 0.8682 (ptp) cc_final: 0.8175 (ptp) REVERT: A 2361 MET cc_start: 0.9068 (ttm) cc_final: 0.8866 (ttm) REVERT: A 2461 MET cc_start: 0.9030 (mtt) cc_final: 0.8617 (mtt) REVERT: A 2576 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.8987 (ptm160) REVERT: A 3006 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: A 3008 MET cc_start: 0.9150 (mmm) cc_final: 0.8905 (tpp) REVERT: A 3073 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 3077 ASP cc_start: 0.9202 (m-30) cc_final: 0.8688 (m-30) REVERT: A 3521 ASP cc_start: 0.8627 (p0) cc_final: 0.8397 (p0) REVERT: A 3791 MET cc_start: 0.9158 (mmp) cc_final: 0.8955 (mmm) REVERT: A 3819 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9071 (pttp) REVERT: A 3933 GLU cc_start: 0.9140 (pt0) cc_final: 0.8628 (pt0) REVERT: A 3990 LEU cc_start: 0.9032 (tp) cc_final: 0.8767 (tp) REVERT: A 4002 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9017 (mt) REVERT: A 4004 MET cc_start: 0.8523 (tmm) cc_final: 0.7841 (tpt) REVERT: A 4030 ILE cc_start: 0.8877 (mm) cc_final: 0.8604 (mm) REVERT: A 4043 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7918 (mpp) REVERT: A 4095 MET cc_start: 0.6910 (tpp) cc_final: 0.6313 (tpp) REVERT: A 4311 LEU cc_start: 0.9336 (pp) cc_final: 0.8941 (mm) REVERT: A 4377 MET cc_start: 0.7487 (tpt) cc_final: 0.7176 (mtm) outliers start: 92 outliers final: 51 residues processed: 308 average time/residue: 0.1576 time to fit residues: 80.1114 Evaluate side-chains 283 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 2145 MET Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2339 VAL 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 2576 ARG 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 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 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 3593 SER Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3677 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 3892 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 120 optimal weight: 8.9990 chunk 100 optimal weight: 0.3980 chunk 31 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1790 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN A2857 HIS A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3792 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.068654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053577 restraints weight = 117165.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055141 restraints weight = 63492.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.056186 restraints weight = 42619.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.056857 restraints weight = 32534.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057295 restraints weight = 27244.100| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24999 Z= 0.140 Angle : 0.591 12.117 33895 Z= 0.291 Chirality : 0.041 0.498 3806 Planarity : 0.004 0.048 4343 Dihedral : 4.937 99.350 3350 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.19 % Allowed : 21.11 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.16), residues: 3019 helix: 2.12 (0.12), residues: 1796 sheet: -1.11 (0.35), residues: 211 loop : 0.26 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2948 TYR 0.029 0.001 TYR A2674 PHE 0.015 0.001 PHE A2635 TRP 0.023 0.001 TRP A1435 HIS 0.006 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00311 (24999) covalent geometry : angle 0.59122 (33895) hydrogen bonds : bond 0.03808 ( 1455) hydrogen bonds : angle 4.30937 ( 4254) *********************** 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 328 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 242 time to evaluate : 0.986 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: 0.8867 (ttp-170) cc_final: 0.8407 (tpt170) REVERT: A 1589 MET cc_start: 0.9097 (mmm) cc_final: 0.8379 (mtp) REVERT: A 1602 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: A 1657 MET cc_start: 0.8849 (mmm) cc_final: 0.8372 (tpt) REVERT: A 1733 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.6153 (mp) REVERT: A 1820 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8609 (t0) REVERT: A 2012 MET cc_start: 0.9020 (mmt) cc_final: 0.8721 (mmm) REVERT: A 2041 MET cc_start: 0.8650 (mmm) cc_final: 0.8024 (mmm) REVERT: A 2053 MET cc_start: 0.8425 (ttt) cc_final: 0.7841 (tpt) REVERT: A 2054 LEU cc_start: 0.9324 (mt) cc_final: 0.8962 (mt) REVERT: A 2087 ASP cc_start: 0.7791 (t0) cc_final: 0.7337 (p0) REVERT: A 2131 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.9003 (mt) REVERT: A 2145 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8687 (mmm) REVERT: A 2161 LEU cc_start: 0.8607 (tt) cc_final: 0.8314 (mt) REVERT: A 2176 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9098 (t) REVERT: A 2361 MET cc_start: 0.8990 (ttm) cc_final: 0.8750 (ttm) REVERT: A 2461 MET cc_start: 0.9015 (mtt) cc_final: 0.8569 (mtt) REVERT: A 2692 PHE cc_start: 0.8737 (p90) cc_final: 0.8440 (p90) REVERT: A 2965 ARG cc_start: 0.8255 (mtp85) cc_final: 0.8022 (mtp85) REVERT: A 3006 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: A 3073 GLU cc_start: 0.8678 (tm-30) cc_final: 0.7949 (tm-30) REVERT: A 3077 ASP cc_start: 0.9213 (m-30) cc_final: 0.8445 (m-30) REVERT: A 3521 ASP cc_start: 0.8647 (p0) cc_final: 0.8440 (p0) REVERT: A 3601 MET cc_start: 0.9036 (mmm) cc_final: 0.8798 (mmm) REVERT: A 3749 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 3819 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9076 (pttp) REVERT: A 3933 GLU cc_start: 0.9132 (pt0) cc_final: 0.8634 (pt0) REVERT: A 3990 LEU cc_start: 0.9138 (tp) cc_final: 0.8921 (tp) REVERT: A 4002 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9003 (mt) REVERT: A 4004 MET cc_start: 0.8514 (tmm) cc_final: 0.7850 (tpt) REVERT: A 4007 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8837 (ttm) REVERT: A 4030 ILE cc_start: 0.8913 (mm) cc_final: 0.8645 (mm) REVERT: A 4043 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7904 (mpp) REVERT: A 4095 MET cc_start: 0.6957 (tpp) cc_final: 0.6415 (tpp) REVERT: A 4311 LEU cc_start: 0.9336 (pp) cc_final: 0.8964 (mm) outliers start: 86 outliers final: 51 residues processed: 303 average time/residue: 0.1433 time to fit residues: 72.5534 Evaluate side-chains 282 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 219 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 1733 ILE Chi-restraints excluded: chain A residue 1820 ASP 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 2140 SER Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2157 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 2750 THR Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2983 SER 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 3062 LEU Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3593 SER Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3677 ILE 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 3886 LEU Chi-restraints excluded: chain A residue 3992 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 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 4300 ILE Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4402 VAL Chi-restraints excluded: chain A residue 4541 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 89 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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** A2085 HIS A2554 GLN ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A2960 GLN A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.050715 restraints weight = 120363.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052252 restraints weight = 64991.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053241 restraints weight = 43568.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053885 restraints weight = 33552.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054305 restraints weight = 28260.478| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24999 Z= 0.248 Angle : 0.665 11.978 33895 Z= 0.334 Chirality : 0.043 0.460 3806 Planarity : 0.004 0.050 4343 Dihedral : 5.148 102.281 3350 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.93 % Allowed : 20.92 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.16), residues: 3019 helix: 1.97 (0.12), residues: 1793 sheet: -1.17 (0.35), residues: 208 loop : 0.16 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2948 TYR 0.020 0.002 TYR A2674 PHE 0.028 0.002 PHE A3513 TRP 0.031 0.002 TRP A1435 HIS 0.006 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00536 (24999) covalent geometry : angle 0.66519 (33895) hydrogen bonds : bond 0.04168 ( 1455) hydrogen bonds : angle 4.54440 ( 4254) *********************** 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 326 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 220 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1360 ARG cc_start: 0.8846 (ttp-170) cc_final: 0.8249 (tpt170) REVERT: A 1556 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7766 (p0) REVERT: A 1589 MET cc_start: 0.9078 (mmm) cc_final: 0.8367 (mtp) REVERT: A 1733 ILE cc_start: 0.6410 (OUTLIER) cc_final: 0.5974 (mp) REVERT: A 1820 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8632 (t0) REVERT: A 2000 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8586 (tp30) REVERT: A 2041 MET cc_start: 0.8669 (mmm) cc_final: 0.8055 (mmm) REVERT: A 2054 LEU cc_start: 0.9457 (mt) cc_final: 0.9165 (mt) REVERT: A 2087 ASP cc_start: 0.7763 (t0) cc_final: 0.7235 (p0) REVERT: A 2131 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9046 (mp) REVERT: A 2145 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8722 (mmm) REVERT: A 2176 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9125 (t) REVERT: A 2361 MET cc_start: 0.9081 (ttm) cc_final: 0.8818 (ttm) REVERT: A 2692 PHE cc_start: 0.8852 (p90) cc_final: 0.8567 (p90) REVERT: A 2773 MET cc_start: 0.9522 (mtt) cc_final: 0.9088 (ttm) REVERT: A 2799 MET cc_start: 0.8692 (ttt) cc_final: 0.8347 (tpp) REVERT: A 2898 LYS cc_start: 0.8957 (tppt) cc_final: 0.8455 (tppt) REVERT: A 2902 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: A 2965 ARG cc_start: 0.8373 (mtp85) cc_final: 0.7997 (mtp85) REVERT: A 3073 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 3077 ASP cc_start: 0.9241 (m-30) cc_final: 0.8489 (m-30) REVERT: A 3695 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8576 (mtp85) REVERT: A 3819 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9145 (pttp) REVERT: A 3933 GLU cc_start: 0.9170 (pt0) cc_final: 0.8725 (pt0) REVERT: A 4002 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9160 (mp) REVERT: A 4004 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7827 (tpt) REVERT: A 4007 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.9019 (ttm) REVERT: A 4030 ILE cc_start: 0.9031 (mm) cc_final: 0.8771 (mm) REVERT: A 4095 MET cc_start: 0.7554 (tpp) cc_final: 0.6924 (tpp) REVERT: A 4128 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7758 (ppp) REVERT: A 4311 LEU cc_start: 0.9333 (pp) cc_final: 0.8954 (mm) REVERT: A 4377 MET cc_start: 0.7618 (tpt) cc_final: 0.7381 (tpt) outliers start: 106 outliers final: 69 residues processed: 301 average time/residue: 0.1440 time to fit residues: 72.5389 Evaluate side-chains 295 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 212 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 1556 ASP Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1637 LEU 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 1964 GLU Chi-restraints excluded: chain A residue 1993 THR Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2131 LEU 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 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 2341 ILE Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2524 VAL 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 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 2821 LEU Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 2983 SER 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 3114 ASP 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 3610 THR Chi-restraints excluded: chain A residue 3617 ASP Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3695 ARG Chi-restraints excluded: chain A residue 3763 ASP Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3789 ILE 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 3987 ILE Chi-restraints excluded: chain A residue 3992 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4004 MET 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 4190 ILE 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 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 192 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 53 optimal weight: 0.0370 chunk 291 optimal weight: 8.9990 chunk 268 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7858 ------------------------------------------------------------------------------- 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** ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2960 GLN A3175 HIS ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3650 ASN A3792 GLN A4029 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052934 restraints weight = 116974.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054513 restraints weight = 62579.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.055543 restraints weight = 41708.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.056214 restraints weight = 31869.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056665 restraints weight = 26657.849| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2822 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= 0.118 Angle : 0.638 16.325 33895 Z= 0.304 Chirality : 0.042 0.523 3806 Planarity : 0.004 0.046 4343 Dihedral : 4.945 92.585 3350 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.89 % Allowed : 21.77 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.16), residues: 3019 helix: 2.03 (0.12), residues: 1794 sheet: -1.06 (0.35), residues: 212 loop : 0.22 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2921 TYR 0.019 0.001 TYR A2748 PHE 0.019 0.001 PHE A3094 TRP 0.028 0.001 TRP A1435 HIS 0.007 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00254 (24999) covalent geometry : angle 0.63823 (33895) hydrogen bonds : bond 0.03736 ( 1455) hydrogen bonds : angle 4.27528 ( 4254) *********************** 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 320 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 242 time to evaluate : 1.017 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: 0.8880 (ttp-170) cc_final: 0.8445 (tpt170) REVERT: A 1500 HIS cc_start: 0.8795 (m90) cc_final: 0.8533 (m90) REVERT: A 1589 MET cc_start: 0.9072 (mmm) cc_final: 0.8368 (mtp) REVERT: A 1602 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: A 1814 GLU cc_start: 0.8762 (tp30) cc_final: 0.8415 (tm-30) REVERT: A 1820 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8735 (t0) REVERT: A 2000 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8589 (tp30) REVERT: A 2041 MET cc_start: 0.8614 (mmm) cc_final: 0.7974 (mmm) REVERT: A 2053 MET cc_start: 0.8415 (ttt) cc_final: 0.7859 (tpt) REVERT: A 2054 LEU cc_start: 0.9347 (mt) cc_final: 0.8959 (mt) REVERT: A 2087 ASP cc_start: 0.7520 (t0) cc_final: 0.7056 (p0) REVERT: A 2131 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8931 (mt) REVERT: A 2145 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8633 (mmm) REVERT: A 2310 GLU cc_start: 0.8818 (mp0) cc_final: 0.8606 (mp0) REVERT: A 2361 MET cc_start: 0.9020 (ttm) cc_final: 0.8804 (ttm) REVERT: A 2461 MET cc_start: 0.9029 (mtt) cc_final: 0.8598 (mtt) REVERT: A 2692 PHE cc_start: 0.8791 (p90) cc_final: 0.8494 (p90) REVERT: A 2799 MET cc_start: 0.8618 (ttt) cc_final: 0.8314 (tpp) REVERT: A 2965 ARG cc_start: 0.8331 (mtp85) cc_final: 0.7950 (mtp85) REVERT: A 3006 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: A 3073 GLU cc_start: 0.8665 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 3077 ASP cc_start: 0.9206 (m-30) cc_final: 0.8359 (m-30) REVERT: A 3601 MET cc_start: 0.9204 (mmm) cc_final: 0.8920 (mmm) REVERT: A 3815 MET cc_start: 0.9429 (mtp) cc_final: 0.9183 (mtm) REVERT: A 3819 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9102 (pttp) REVERT: A 3933 GLU cc_start: 0.9167 (pt0) cc_final: 0.8718 (pt0) REVERT: A 3946 ASP cc_start: 0.8253 (p0) cc_final: 0.7811 (t0) REVERT: A 4002 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9101 (mp) REVERT: A 4004 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.8003 (tpt) REVERT: A 4007 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8948 (ttm) REVERT: A 4030 ILE cc_start: 0.8950 (mm) cc_final: 0.8692 (mm) REVERT: A 4082 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8718 (mmtm) REVERT: A 4095 MET cc_start: 0.7322 (tpp) cc_final: 0.6782 (tpp) REVERT: A 4128 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7798 (ppp) REVERT: A 4311 LEU cc_start: 0.9310 (pp) cc_final: 0.8926 (mm) REVERT: A 4377 MET cc_start: 0.7357 (tpt) cc_final: 0.6973 (mtm) outliers start: 78 outliers final: 45 residues processed: 300 average time/residue: 0.1497 time to fit residues: 74.5559 Evaluate side-chains 285 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 1927 VAL Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2000 GLU 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 2247 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2335 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 2667 ASN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2983 SER Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3154 LEU 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 3677 ILE 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 3992 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4004 MET Chi-restraints excluded: chain A residue 4007 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 191 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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** ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2930 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.067258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052284 restraints weight = 118211.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053851 restraints weight = 63815.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.054864 restraints weight = 42624.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.055518 restraints weight = 32575.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055950 restraints weight = 27299.817| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24999 Z= 0.152 Angle : 0.636 14.443 33895 Z= 0.308 Chirality : 0.042 0.493 3806 Planarity : 0.004 0.047 4343 Dihedral : 4.938 94.966 3350 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.37 % Allowed : 22.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.16), residues: 3019 helix: 2.09 (0.12), residues: 1781 sheet: -0.94 (0.35), residues: 202 loop : 0.23 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3695 TYR 0.018 0.001 TYR A2748 PHE 0.036 0.001 PHE A3513 TRP 0.030 0.001 TRP A1435 HIS 0.007 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00336 (24999) covalent geometry : angle 0.63642 (33895) hydrogen bonds : bond 0.03772 ( 1455) hydrogen bonds : angle 4.35468 ( 4254) *********************** 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 295 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 231 time to evaluate : 0.979 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: 0.8877 (ttp-170) cc_final: 0.8425 (tpt-90) REVERT: A 1589 MET cc_start: 0.9077 (mmm) cc_final: 0.8347 (mtp) REVERT: A 1602 GLU cc_start: 0.8136 (mp0) cc_final: 0.7741 (mp0) REVERT: A 1657 MET cc_start: 0.8969 (mmm) cc_final: 0.8550 (tpt) REVERT: A 1814 GLU cc_start: 0.8820 (tp30) cc_final: 0.8490 (tm-30) REVERT: A 1820 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8742 (t0) REVERT: A 2000 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8561 (tp30) REVERT: A 2053 MET cc_start: 0.8425 (ttt) cc_final: 0.7873 (tpt) REVERT: A 2054 LEU cc_start: 0.9373 (mt) cc_final: 0.8993 (mt) REVERT: A 2087 ASP cc_start: 0.7630 (t0) cc_final: 0.7222 (p0) REVERT: A 2145 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8634 (mmm) REVERT: A 2304 ASP cc_start: 0.7679 (t0) cc_final: 0.7472 (t0) REVERT: A 2310 GLU cc_start: 0.8873 (mp0) cc_final: 0.8646 (mp0) REVERT: A 2373 MET cc_start: 0.8740 (ptp) cc_final: 0.8385 (ptp) REVERT: A 2461 MET cc_start: 0.9037 (mtt) cc_final: 0.8627 (mtt) REVERT: A 2659 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9104 (tp) REVERT: A 2674 TYR cc_start: 0.6472 (m-10) cc_final: 0.6220 (m-10) REVERT: A 2692 PHE cc_start: 0.8780 (p90) cc_final: 0.8502 (p90) REVERT: A 2799 MET cc_start: 0.8623 (ttt) cc_final: 0.8296 (tpp) REVERT: A 2965 ARG cc_start: 0.8323 (mtp85) cc_final: 0.7936 (mtp85) REVERT: A 3006 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: A 3073 GLU cc_start: 0.8647 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 3077 ASP cc_start: 0.9193 (m-30) cc_final: 0.8332 (m-30) REVERT: A 3169 MET cc_start: 0.6921 (mmm) cc_final: 0.6561 (mmm) REVERT: A 3815 MET cc_start: 0.9436 (mtp) cc_final: 0.9184 (mtm) REVERT: A 3933 GLU cc_start: 0.9182 (pt0) cc_final: 0.8759 (pt0) REVERT: A 3946 ASP cc_start: 0.8177 (p0) cc_final: 0.7822 (t0) REVERT: A 4002 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9133 (mp) REVERT: A 4004 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7919 (tpt) REVERT: A 4007 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8992 (ttm) REVERT: A 4030 ILE cc_start: 0.8978 (mm) cc_final: 0.8720 (mm) REVERT: A 4095 MET cc_start: 0.7433 (tpp) cc_final: 0.6905 (tpp) REVERT: A 4128 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7835 (ppp) REVERT: A 4311 LEU cc_start: 0.9315 (pp) cc_final: 0.8920 (mm) REVERT: A 4377 MET cc_start: 0.7404 (tpt) cc_final: 0.6985 (mtm) outliers start: 64 outliers final: 49 residues processed: 277 average time/residue: 0.1334 time to fit residues: 62.1307 Evaluate side-chains 277 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 1993 THR Chi-restraints excluded: chain A residue 2000 GLU 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 2247 VAL Chi-restraints excluded: chain A residue 2325 LEU Chi-restraints excluded: chain A residue 2335 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 2659 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2903 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 2983 SER Chi-restraints excluded: chain A residue 3006 GLU 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 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 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 4004 MET Chi-restraints excluded: chain A residue 4007 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 94 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3584 ASN ** 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 = 0.3413 r_free = 0.3413 target = 0.066793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051899 restraints weight = 118787.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053447 restraints weight = 64000.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.054463 restraints weight = 42778.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055089 restraints weight = 32685.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.055523 restraints weight = 27487.275| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24999 Z= 0.164 Angle : 0.656 13.839 33895 Z= 0.318 Chirality : 0.042 0.492 3806 Planarity : 0.004 0.048 4343 Dihedral : 4.961 94.051 3350 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.67 % Allowed : 22.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.16), residues: 3019 helix: 2.07 (0.12), residues: 1782 sheet: -1.09 (0.34), residues: 219 loop : 0.18 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3695 TYR 0.018 0.001 TYR A2748 PHE 0.016 0.001 PHE A3094 TRP 0.033 0.001 TRP A1435 HIS 0.008 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00364 (24999) covalent geometry : angle 0.65643 (33895) hydrogen bonds : bond 0.03797 ( 1455) hydrogen bonds : angle 4.39696 ( 4254) *********************** 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 296 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 224 time to evaluate : 0.984 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: 0.8877 (ttp-170) cc_final: 0.8439 (tpt-90) REVERT: A 1424 TRP cc_start: 0.7325 (m-10) cc_final: 0.7090 (m-10) REVERT: A 1486 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8635 (tp) REVERT: A 1589 MET cc_start: 0.9049 (mmm) cc_final: 0.8313 (mtp) REVERT: A 1602 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: A 1820 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8701 (t0) REVERT: A 2000 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8529 (tp30) REVERT: A 2012 MET cc_start: 0.9024 (mmt) cc_final: 0.8714 (mmm) REVERT: A 2053 MET cc_start: 0.8433 (ttt) cc_final: 0.7884 (tpt) REVERT: A 2054 LEU cc_start: 0.9393 (mt) cc_final: 0.9003 (mt) REVERT: A 2087 ASP cc_start: 0.7606 (t0) cc_final: 0.7266 (p0) REVERT: A 2145 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8628 (mmm) REVERT: A 2176 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9066 (t) REVERT: A 2310 GLU cc_start: 0.8908 (mp0) cc_final: 0.8683 (mp0) REVERT: A 2361 MET cc_start: 0.8991 (ttm) cc_final: 0.8624 (ttm) REVERT: A 2373 MET cc_start: 0.8772 (ptp) cc_final: 0.8482 (ptp) REVERT: A 2461 MET cc_start: 0.9053 (mtt) cc_final: 0.8654 (mtt) REVERT: A 2659 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9067 (tp) REVERT: A 2674 TYR cc_start: 0.6554 (m-10) cc_final: 0.6354 (m-10) REVERT: A 2692 PHE cc_start: 0.8808 (p90) cc_final: 0.8528 (p90) REVERT: A 2799 MET cc_start: 0.8631 (ttt) cc_final: 0.8288 (tpp) REVERT: A 2965 ARG cc_start: 0.8345 (mtp85) cc_final: 0.7942 (mtp85) REVERT: A 3006 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: A 3073 GLU cc_start: 0.8659 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 3077 ASP cc_start: 0.9187 (m-30) cc_final: 0.8316 (m-30) REVERT: A 3169 MET cc_start: 0.6930 (mmm) cc_final: 0.6563 (mmm) REVERT: A 3815 MET cc_start: 0.9438 (mtp) cc_final: 0.9158 (mtm) REVERT: A 3933 GLU cc_start: 0.9172 (pt0) cc_final: 0.8771 (pt0) REVERT: A 3946 ASP cc_start: 0.8251 (p0) cc_final: 0.7997 (t0) REVERT: A 4002 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9150 (mp) REVERT: A 4004 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7929 (tpt) REVERT: A 4007 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8764 (ttm) REVERT: A 4030 ILE cc_start: 0.8982 (mm) cc_final: 0.8728 (mm) REVERT: A 4095 MET cc_start: 0.7632 (tpp) cc_final: 0.7194 (tpp) REVERT: A 4128 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7827 (ppp) REVERT: A 4311 LEU cc_start: 0.9282 (pp) cc_final: 0.8853 (mm) REVERT: A 4377 MET cc_start: 0.7514 (tpt) cc_final: 0.7122 (mtm) outliers start: 72 outliers final: 54 residues processed: 276 average time/residue: 0.1519 time to fit residues: 69.6888 Evaluate side-chains 281 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1421 HIS Chi-restraints excluded: chain A residue 1486 LEU 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 1993 THR Chi-restraints excluded: chain A residue 2000 GLU 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 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 2659 LEU Chi-restraints excluded: chain A residue 2667 ASN Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2903 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 2983 SER Chi-restraints excluded: chain A residue 3006 GLU 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 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 3717 LEU 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 3824 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3992 LEU Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4004 MET 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 Chi-restraints excluded: chain A residue 4541 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 150 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 232 optimal weight: 0.0670 chunk 145 optimal weight: 3.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.067943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052960 restraints weight = 117544.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054551 restraints weight = 62962.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055568 restraints weight = 41823.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.056231 restraints weight = 31977.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056654 restraints weight = 26795.318| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24999 Z= 0.121 Angle : 0.658 12.953 33895 Z= 0.312 Chirality : 0.042 0.511 3806 Planarity : 0.004 0.046 4343 Dihedral : 4.864 89.100 3350 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.34 % Allowed : 22.77 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.16), residues: 3019 helix: 2.11 (0.12), residues: 1776 sheet: -1.23 (0.33), residues: 227 loop : 0.28 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3695 TYR 0.020 0.001 TYR A2748 PHE 0.017 0.001 PHE A3513 TRP 0.030 0.001 TRP A1435 HIS 0.006 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00267 (24999) covalent geometry : angle 0.65819 (33895) hydrogen bonds : bond 0.03639 ( 1455) hydrogen bonds : angle 4.31926 ( 4254) ********************** 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 296 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 1.078 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: 0.8865 (ttp-170) cc_final: 0.8445 (tpt-90) REVERT: A 1589 MET cc_start: 0.9052 (mmm) cc_final: 0.8210 (mtm) REVERT: A 1602 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 1657 MET cc_start: 0.8998 (mmm) cc_final: 0.8566 (tpt) REVERT: A 1820 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8725 (t0) REVERT: A 2000 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8611 (tp30) REVERT: A 2012 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8593 (mmm) REVERT: A 2053 MET cc_start: 0.8425 (ttt) cc_final: 0.7840 (tpt) REVERT: A 2054 LEU cc_start: 0.9351 (mt) cc_final: 0.8957 (mt) REVERT: A 2087 ASP cc_start: 0.7512 (t0) cc_final: 0.7161 (p0) REVERT: A 2161 LEU cc_start: 0.8803 (mt) cc_final: 0.8593 (mt) REVERT: A 2310 GLU cc_start: 0.8952 (mp0) cc_final: 0.8679 (mp0) REVERT: A 2361 MET cc_start: 0.9008 (ttm) cc_final: 0.8676 (ttm) REVERT: A 2373 MET cc_start: 0.8729 (ptp) cc_final: 0.8445 (ptp) REVERT: A 2461 MET cc_start: 0.9038 (mtt) cc_final: 0.8645 (mtt) REVERT: A 2659 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9046 (tp) REVERT: A 2674 TYR cc_start: 0.6535 (m-10) cc_final: 0.6202 (m-10) REVERT: A 2692 PHE cc_start: 0.8792 (p90) cc_final: 0.8521 (p90) REVERT: A 2799 MET cc_start: 0.8594 (ttt) cc_final: 0.8208 (tpp) REVERT: A 2965 ARG cc_start: 0.8372 (mtp85) cc_final: 0.8003 (mtp85) REVERT: A 3006 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: A 3073 GLU cc_start: 0.8538 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 3077 ASP cc_start: 0.9177 (m-30) cc_final: 0.8269 (m-30) REVERT: A 3169 MET cc_start: 0.6755 (mmm) cc_final: 0.6426 (mmm) REVERT: A 3195 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9075 (mp0) REVERT: A 3601 MET cc_start: 0.9383 (mmm) cc_final: 0.9118 (mmm) REVERT: A 3786 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8669 (pt0) REVERT: A 3815 MET cc_start: 0.9411 (mtp) cc_final: 0.9198 (mtm) REVERT: A 3933 GLU cc_start: 0.9162 (pt0) cc_final: 0.8760 (pt0) REVERT: A 3946 ASP cc_start: 0.8294 (p0) cc_final: 0.8090 (t0) REVERT: A 4002 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9131 (mp) REVERT: A 4007 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8943 (ttm) REVERT: A 4030 ILE cc_start: 0.8946 (mm) cc_final: 0.8666 (mm) REVERT: A 4095 MET cc_start: 0.7568 (tpp) cc_final: 0.7176 (tpp) REVERT: A 4128 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7861 (ppp) REVERT: A 4311 LEU cc_start: 0.9323 (pp) cc_final: 0.8902 (mm) REVERT: A 4377 MET cc_start: 0.7253 (tpt) cc_final: 0.6850 (mtm) outliers start: 63 outliers final: 46 residues processed: 278 average time/residue: 0.1514 time to fit residues: 71.0325 Evaluate side-chains 277 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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 2247 VAL 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 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 2659 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 2903 GLU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 2983 SER Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3115 LEU 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 3717 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3788 ASP Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3992 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 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 68 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 205 optimal weight: 0.0170 chunk 86 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 269 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1593 ASN ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN ** 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 = 0.3422 r_free = 0.3422 target = 0.067388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052443 restraints weight = 117924.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054036 restraints weight = 62271.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055067 restraints weight = 41002.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.055748 restraints weight = 31002.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056208 restraints weight = 25740.026| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24999 Z= 0.119 Angle : 0.660 12.535 33895 Z= 0.314 Chirality : 0.042 0.506 3806 Planarity : 0.004 0.045 4343 Dihedral : 4.837 88.050 3350 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.00 % Allowed : 23.26 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.16), residues: 3019 helix: 2.09 (0.12), residues: 1783 sheet: -1.25 (0.33), residues: 227 loop : 0.21 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3695 TYR 0.021 0.001 TYR A2748 PHE 0.036 0.001 PHE A3513 TRP 0.033 0.001 TRP A1435 HIS 0.007 0.001 HIS A2918 Details of bonding type rmsd covalent geometry : bond 0.00263 (24999) covalent geometry : angle 0.66032 (33895) hydrogen bonds : bond 0.03638 ( 1455) hydrogen bonds : angle 4.30694 ( 4254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4174.49 seconds wall clock time: 73 minutes 2.90 seconds (4382.90 seconds total)