Starting phenix.real_space_refine on Fri Jun 20 16:34:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bn0_44717/06_2025/9bn0_44717.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bn0_44717/06_2025/9bn0_44717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bn0_44717/06_2025/9bn0_44717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bn0_44717/06_2025/9bn0_44717.map" model { file = "/net/cci-nas-00/data/ceres_data/9bn0_44717/06_2025/9bn0_44717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bn0_44717/06_2025/9bn0_44717.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 117 5.16 5 C 14925 2.51 5 N 4058 2.21 5 O 4387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23497 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 23384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2909, 23384 Classifications: {'peptide': 2909} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 127, 'TRANS': 2778} Chain breaks: 3 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 12.93, per 1000 atoms: 0.55 Number of scatterers: 23497 At special positions: 0 Unit cell: (119.784, 165.354, 153.636, 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 117 16.00 P 9 15.00 Mg 1 11.99 O 4387 8.00 N 4058 7.00 C 14925 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: 6.48 Conformation dependent library (CDL) restraints added in 3.0 seconds 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5528 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 19 sheets defined 62.6% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'A' and resid 1461 through 1472 Processing helix chain 'A' and resid 1489 through 1508 removed outlier: 3.653A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1515 removed outlier: 5.176A pdb=" N TYR A1512 " --> pdb=" O LEU A1509 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1515 " --> pdb=" O TYR A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1553 removed outlier: 3.791A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 Processing helix chain 'A' and resid 1561 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 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.874A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.685A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1773 removed outlier: 3.609A pdb=" N GLY A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.618A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.629A 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 1923 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 1984 Processing helix chain 'A' and resid 1985 through 1987 No H-bonds generated for 'chain 'A' and resid 1985 through 1987' Processing helix chain 'A' and resid 2029 through 2033 Processing helix chain 'A' and resid 2045 through 2057 removed outlier: 3.503A pdb=" N MET A2053 " --> pdb=" O ILE A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2079 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 3.517A pdb=" N ILE A2136 " --> pdb=" O PRO A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.229A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 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 Processing helix chain 'A' and resid 2315 through 2320 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 removed outlier: 3.523A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2400 removed outlier: 4.133A pdb=" N ARG A2398 " --> pdb=" O ALA A2394 " (cutoff:3.500A) 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 removed outlier: 3.753A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.510A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.787A pdb=" N GLU A2578 " --> pdb=" O THR A2574 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2610 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.968A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2757 removed outlier: 3.824A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2761 through 2764 removed outlier: 4.029A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2761 through 2764' Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2796 through 2811 Processing helix chain 'A' and resid 2817 through 2833 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.855A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2927 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.584A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3002 through 3015 removed outlier: 3.963A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 4.335A 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 3061 removed outlier: 3.591A pdb=" N LYS A3052 " --> pdb=" O GLU A3048 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A3060 " --> pdb=" O SER A3056 " (cutoff:3.500A) 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 removed outlier: 3.673A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 4.759A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3694 Processing helix chain 'A' and resid 3706 through 3721 Processing helix chain 'A' and resid 3721 through 3734 Processing helix chain 'A' and resid 3736 through 3755 removed outlier: 4.236A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3762 Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 4.194A pdb=" N LEU A3770 " --> pdb=" O ILE A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3818 removed outlier: 3.505A pdb=" N VAL A3790 " --> pdb=" O GLU A3786 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3851 through 3872 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 Processing helix chain 'A' and resid 3941 through 3945 removed outlier: 3.701A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3952 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 4.079A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4015 through 4017 No H-bonds generated for 'chain 'A' and resid 4015 through 4017' Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.579A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.587A 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 removed outlier: 3.908A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.940A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4089 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 4196 removed outlier: 4.176A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR A4196 " --> pdb=" O GLU A4192 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4326 through 4348 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4407 removed outlier: 4.288A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP A4407 " --> pdb=" O GLU A4403 " (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 4500 removed outlier: 3.514A pdb=" N GLU A4484 " --> pdb=" O SER A4480 " (cutoff:3.500A) Processing helix chain 'A' and resid 4501 through 4506 removed outlier: 4.099A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4501 through 4506' Processing helix chain 'A' and resid 4516 through 4532 Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.610A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 3.663A pdb=" N SER A1677 " --> pdb=" O SER A1663 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) 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 1930 removed outlier: 6.248A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.298A 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: 7.106A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (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 2710 through 2712 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 3.513A pdb=" N VAL A2660 " --> pdb=" O GLU A2616 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 6.800A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.306A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.255A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3661 through 3662 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.486A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A4128 " --> pdb=" O MET A4043 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ARG A4143 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A4044 " --> pdb=" O ARG A4143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.975A 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: 3.923A pdb=" N VAL A4509 " --> pdb=" O GLY A4559 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A4561 " --> pdb=" O VAL A4509 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4568 through 4570 removed outlier: 3.940A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1359 hydrogen bonds defined for protein. 3954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.00 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6532 1.33 - 1.45: 3946 1.45 - 1.57: 13313 1.57 - 1.69: 14 1.69 - 1.81: 196 Bond restraints: 24001 Sorted by residual: bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C5 ADP A4704 " pdb=" C6 ADP A4704 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 23996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 31830 2.28 - 4.55: 627 4.55 - 6.83: 60 6.83 - 9.10: 19 9.10 - 11.38: 13 Bond angle restraints: 32549 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 130.46 9.41 1.00e+00 1.00e+00 8.86e+01 angle pdb=" PA ATP A4702 " pdb=" O3A ATP A4702 " pdb=" PB ATP A4702 " ideal model delta sigma weight residual 136.83 129.36 7.47 1.00e+00 1.00e+00 5.57e+01 angle pdb=" N VAL A3129 " pdb=" CA VAL A3129 " pdb=" C VAL A3129 " ideal model delta sigma weight residual 113.43 107.76 5.67 1.09e+00 8.42e-01 2.70e+01 angle pdb=" N GLU A2996 " pdb=" CA GLU A2996 " pdb=" C GLU A2996 " ideal model delta sigma weight residual 113.38 108.26 5.12 1.23e+00 6.61e-01 1.73e+01 angle pdb=" N PRO A3684 " pdb=" CD PRO A3684 " pdb=" CG PRO A3684 " ideal model delta sigma weight residual 103.20 97.28 5.92 1.50e+00 4.44e-01 1.56e+01 ... (remaining 32544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.13: 13377 25.13 - 50.26: 999 50.26 - 75.40: 156 75.40 - 100.53: 24 100.53 - 125.66: 2 Dihedral angle restraints: 14558 sinusoidal: 6045 harmonic: 8513 Sorted by residual: dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual 300.00 174.34 125.66 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" O1B ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " pdb=" PA ADP A4704 " ideal model delta sinusoidal sigma weight residual -60.00 55.34 -115.34 1 2.00e+01 2.50e-03 3.43e+01 dihedral pdb=" CA TRP A3093 " pdb=" C TRP A3093 " pdb=" N PHE A3094 " pdb=" CA PHE A3094 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 14555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2723 0.041 - 0.082: 599 0.082 - 0.124: 258 0.124 - 0.165: 51 0.165 - 0.206: 20 Chirality restraints: 3651 Sorted by residual: chirality pdb=" CA ILE A1571 " pdb=" N ILE A1571 " pdb=" C ILE A1571 " pdb=" CB ILE A1571 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A1611 " pdb=" N ILE A1611 " pdb=" C ILE A1611 " pdb=" CB ILE A1611 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL A2907 " pdb=" N VAL A2907 " pdb=" C VAL A2907 " pdb=" CB VAL A2907 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3648 not shown) Planarity restraints: 4175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A3695 " -0.335 9.50e-02 1.11e+02 1.50e-01 1.38e+01 pdb=" NE ARG A3695 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A3695 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A3695 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A3695 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A4023 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO A4024 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A4024 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A4024 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2797 " 0.223 9.50e-02 1.11e+02 1.00e-01 6.15e+00 pdb=" NE ARG A2797 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A2797 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A2797 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A2797 " 0.008 2.00e-02 2.50e+03 ... (remaining 4172 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 5 2.19 - 2.87: 8582 2.87 - 3.55: 35244 3.55 - 4.22: 52736 4.22 - 4.90: 95015 Nonbonded interactions: 191582 Sorted by model distance: nonbonded pdb=" O1B ATP A4702 " pdb="MG MG A4705 " model vdw 1.515 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4705 " model vdw 1.884 2.170 nonbonded pdb=" ND1 HIS A3151 " pdb=" OH TYR A3516 " model vdw 2.148 3.120 nonbonded pdb=" N GLU A2970 " pdb=" OE1 GLU A2970 " model vdw 2.190 3.120 nonbonded pdb=" OH TYR A2265 " pdb=" O TRP A2311 " model vdw 2.191 3.040 ... (remaining 191577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.980 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 59.060 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 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 : 0.005 0.110 24001 Z= 0.298 Angle : 0.718 11.376 32549 Z= 0.430 Chirality : 0.045 0.206 3651 Planarity : 0.005 0.150 4175 Dihedral : 16.967 125.659 9030 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 0.46 % Allowed : 19.47 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.16), residues: 2901 helix: 1.92 (0.13), residues: 1654 sheet: -1.01 (0.32), residues: 265 loop : 0.18 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1523 HIS 0.006 0.001 HIS A3155 PHE 0.021 0.001 PHE A1938 TYR 0.027 0.001 TYR A1546 ARG 0.007 0.000 ARG A3910 Details of bonding type rmsd hydrogen bonds : bond 0.13610 ( 1359) hydrogen bonds : angle 5.59690 ( 3954) covalent geometry : bond 0.00476 (24001) covalent geometry : angle 0.71751 (32549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 766 time to evaluate : 2.714 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2069 ILE cc_start: 0.8680 (tp) cc_final: 0.8372 (tp) REVERT: A 2666 ILE cc_start: 0.7135 (mm) cc_final: 0.6458 (mt) REVERT: A 3171 ILE cc_start: 0.7435 (mm) cc_final: 0.7151 (mt) REVERT: A 3584 ASN cc_start: 0.5407 (m-40) cc_final: 0.5032 (m-40) REVERT: A 3815 MET cc_start: 0.6789 (mtm) cc_final: 0.6487 (mtp) REVERT: A 4008 PHE cc_start: 0.6864 (t80) cc_final: 0.6528 (t80) outliers start: 12 outliers final: 2 residues processed: 772 average time/residue: 0.4078 time to fit residues: 473.5619 Evaluate side-chains 379 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 377 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 2747 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 0.6980 chunk 219 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 87 optimal weight: 0.0060 chunk 138 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1481 GLN A1653 HIS ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2424 GLN A2468 ASN A2677 GLN A2752 ASN A2857 HIS A3032 GLN A3047 HIS A3135 GLN A3188 HIS ** A3535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN A3845 ASN A3852 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4085 ASN ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4137 ASN A4397 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.134029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.107576 restraints weight = 67134.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.110337 restraints weight = 34394.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.112157 restraints weight = 22426.962| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24001 Z= 0.153 Angle : 0.665 15.185 32549 Z= 0.326 Chirality : 0.041 0.192 3651 Planarity : 0.004 0.055 4175 Dihedral : 6.170 120.480 3236 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Rotamer: Outliers : 2.79 % Allowed : 22.07 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2901 helix: 1.99 (0.13), residues: 1665 sheet: -0.94 (0.32), residues: 253 loop : 0.23 (0.21), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A2234 HIS 0.011 0.001 HIS A2964 PHE 0.037 0.002 PHE A2751 TYR 0.022 0.002 TYR A3103 ARG 0.008 0.001 ARG A2843 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 1359) hydrogen bonds : angle 4.55479 ( 3954) covalent geometry : bond 0.00344 (24001) covalent geometry : angle 0.66466 (32549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 414 time to evaluate : 2.896 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: symmetry clash REVERT: A 1542 ARG cc_start: 0.7641 (ptp-110) cc_final: 0.7266 (ptp-170) REVERT: A 1814 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 1841 GLN cc_start: 0.8100 (mp10) cc_final: 0.7484 (mp10) REVERT: A 1861 MET cc_start: 0.7814 (ttt) cc_final: 0.7439 (ttt) REVERT: A 1967 MET cc_start: 0.7657 (mtp) cc_final: 0.7372 (ttt) REVERT: A 2012 MET cc_start: 0.8805 (tmm) cc_final: 0.8524 (tmm) REVERT: A 2069 ILE cc_start: 0.9174 (tp) cc_final: 0.8832 (tp) REVERT: A 2481 MET cc_start: 0.7855 (pmm) cc_final: 0.7438 (ttm) REVERT: A 2759 ILE cc_start: 0.5931 (OUTLIER) cc_final: 0.5493 (mm) REVERT: A 2851 ASP cc_start: 0.9015 (m-30) cc_final: 0.8582 (m-30) REVERT: A 2867 MET cc_start: 0.6955 (mtt) cc_final: 0.6537 (tpt) REVERT: A 2961 ILE cc_start: 0.8359 (pt) cc_final: 0.7751 (pt) REVERT: A 3706 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8287 (m) REVERT: A 3819 LYS cc_start: 0.8773 (ptpt) cc_final: 0.8516 (ptpt) REVERT: A 3882 THR cc_start: 0.9227 (m) cc_final: 0.8968 (p) REVERT: A 4004 MET cc_start: 0.7779 (tpp) cc_final: 0.7258 (tpt) REVERT: A 4043 MET cc_start: 0.9100 (mmm) cc_final: 0.8848 (mmm) REVERT: A 4079 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7589 (mm-40) REVERT: A 4082 LYS cc_start: 0.7479 (mttt) cc_final: 0.6962 (ptpp) REVERT: A 4116 LEU cc_start: 0.7045 (mt) cc_final: 0.6630 (mp) REVERT: A 4381 HIS cc_start: 0.5845 (t-90) cc_final: 0.5335 (t-90) REVERT: A 4564 LYS cc_start: 0.8702 (mppt) cc_final: 0.8371 (mttp) outliers start: 72 outliers final: 28 residues processed: 464 average time/residue: 0.3834 time to fit residues: 279.2415 Evaluate side-chains 358 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 328 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1847 ASP Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2339 VAL Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3093 TRP Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 55 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 270 optimal weight: 0.0060 chunk 177 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 9 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1566 GLN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN A2857 HIS A3047 HIS A3584 ASN ** A3700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4085 ASN A4397 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.130042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.102866 restraints weight = 68423.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.105491 restraints weight = 35545.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.107251 restraints weight = 23506.281| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24001 Z= 0.154 Angle : 0.631 11.817 32549 Z= 0.308 Chirality : 0.041 0.281 3651 Planarity : 0.004 0.048 4175 Dihedral : 6.036 119.388 3234 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.86 % Rotamer: Outliers : 3.21 % Allowed : 21.33 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.16), residues: 2901 helix: 2.03 (0.13), residues: 1667 sheet: -1.12 (0.31), residues: 269 loop : 0.36 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2584 HIS 0.018 0.001 HIS A3047 PHE 0.026 0.002 PHE A3832 TYR 0.018 0.002 TYR A2735 ARG 0.014 0.001 ARG A4092 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 1359) hydrogen bonds : angle 4.39106 ( 3954) covalent geometry : bond 0.00350 (24001) covalent geometry : angle 0.63120 (32549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 362 time to evaluate : 2.889 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 1611 ILE cc_start: 0.8014 (mm) cc_final: 0.7734 (mm) REVERT: A 1652 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7510 (pttm) REVERT: A 1657 MET cc_start: 0.7049 (mmm) cc_final: 0.6745 (mmm) REVERT: A 1837 GLU cc_start: 0.7825 (tp30) cc_final: 0.7424 (tp30) REVERT: A 1841 GLN cc_start: 0.8373 (mp10) cc_final: 0.7868 (mp10) REVERT: A 1861 MET cc_start: 0.7879 (ttt) cc_final: 0.7441 (ttt) REVERT: A 2069 ILE cc_start: 0.9157 (tp) cc_final: 0.8888 (tp) REVERT: A 2294 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6374 (mp0) REVERT: A 2314 ASN cc_start: 0.8205 (m-40) cc_final: 0.7841 (m-40) REVERT: A 2481 MET cc_start: 0.7834 (pmm) cc_final: 0.7540 (ttm) REVERT: A 2594 CYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7219 (t) REVERT: A 2759 ILE cc_start: 0.5826 (OUTLIER) cc_final: 0.5396 (mm) REVERT: A 2851 ASP cc_start: 0.9090 (m-30) cc_final: 0.8586 (m-30) REVERT: A 2867 MET cc_start: 0.7226 (mtt) cc_final: 0.6735 (tpt) REVERT: A 2961 ILE cc_start: 0.8363 (pt) cc_final: 0.7991 (pt) REVERT: A 2975 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: A 2977 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7675 (ttp-110) REVERT: A 3016 GLU cc_start: 0.7446 (pp20) cc_final: 0.7121 (tm-30) REVERT: A 3029 LEU cc_start: 0.8727 (tp) cc_final: 0.8439 (tt) REVERT: A 3030 MET cc_start: 0.6968 (mmm) cc_final: 0.6587 (mmm) REVERT: A 3126 MET cc_start: 0.3209 (pmm) cc_final: 0.2807 (pmm) REVERT: A 3169 MET cc_start: 0.7991 (mmt) cc_final: 0.7622 (mmt) REVERT: A 3176 TYR cc_start: 0.8592 (t80) cc_final: 0.8293 (t80) REVERT: A 3507 CYS cc_start: 0.8661 (m) cc_final: 0.8104 (t) REVERT: A 3552 TYR cc_start: 0.8170 (t80) cc_final: 0.7717 (t80) REVERT: A 3584 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7780 (t0) REVERT: A 3813 PHE cc_start: 0.8506 (m-10) cc_final: 0.8093 (m-10) REVERT: A 3819 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8529 (ptpt) REVERT: A 4004 MET cc_start: 0.7922 (tpp) cc_final: 0.7520 (tpt) REVERT: A 4042 LEU cc_start: 0.8205 (mp) cc_final: 0.7815 (mp) REVERT: A 4043 MET cc_start: 0.9135 (mmm) cc_final: 0.8662 (mmm) REVERT: A 4128 MET cc_start: 0.7811 (ptp) cc_final: 0.7178 (ptp) REVERT: A 4158 LEU cc_start: 0.9288 (mt) cc_final: 0.9087 (mt) REVERT: A 4381 HIS cc_start: 0.5975 (t-90) cc_final: 0.5519 (t-90) REVERT: A 4429 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7834 (mm-40) outliers start: 83 outliers final: 43 residues processed: 418 average time/residue: 0.3427 time to fit residues: 233.5735 Evaluate side-chains 372 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 324 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1941 MET Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2339 VAL Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2975 ASP Chi-restraints excluded: chain A residue 3093 TRP Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3584 ASN Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 259 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 240 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 ASN A2314 ASN A2442 GLN A2857 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4397 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.127268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.100356 restraints weight = 67559.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.102985 restraints weight = 34623.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.104753 restraints weight = 22777.592| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24001 Z= 0.147 Angle : 0.606 10.402 32549 Z= 0.297 Chirality : 0.041 0.269 3651 Planarity : 0.004 0.057 4175 Dihedral : 5.918 118.365 3233 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Rotamer: Outliers : 3.10 % Allowed : 22.42 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.16), residues: 2901 helix: 2.04 (0.13), residues: 1660 sheet: -1.09 (0.31), residues: 267 loop : 0.34 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A2584 HIS 0.006 0.001 HIS A2439 PHE 0.027 0.002 PHE A4613 TYR 0.015 0.001 TYR A3516 ARG 0.007 0.001 ARG A2273 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 1359) hydrogen bonds : angle 4.26555 ( 3954) covalent geometry : bond 0.00332 (24001) covalent geometry : angle 0.60601 (32549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 349 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1615 LEU cc_start: 0.8517 (tp) cc_final: 0.8237 (pp) REVERT: A 1665 ILE cc_start: 0.8085 (mm) cc_final: 0.7707 (mt) REVERT: A 1837 GLU cc_start: 0.7821 (tp30) cc_final: 0.7394 (tp30) REVERT: A 1841 GLN cc_start: 0.8487 (mp10) cc_final: 0.8043 (mp10) REVERT: A 1861 MET cc_start: 0.8000 (ttt) cc_final: 0.7492 (ttt) REVERT: A 2012 MET cc_start: 0.8851 (tmm) cc_final: 0.8533 (tmm) REVERT: A 2263 HIS cc_start: 0.8185 (m90) cc_final: 0.7975 (m90) REVERT: A 2294 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6639 (mp0) REVERT: A 2481 MET cc_start: 0.7839 (pmm) cc_final: 0.7344 (ttm) REVERT: A 2487 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: A 2591 LEU cc_start: 0.8908 (mp) cc_final: 0.8637 (mp) REVERT: A 2594 CYS cc_start: 0.7823 (t) cc_final: 0.7543 (t) REVERT: A 2759 ILE cc_start: 0.5889 (OUTLIER) cc_final: 0.5464 (mm) REVERT: A 2851 ASP cc_start: 0.9035 (m-30) cc_final: 0.8461 (m-30) REVERT: A 2867 MET cc_start: 0.7284 (mtt) cc_final: 0.6784 (tpt) REVERT: A 2959 TYR cc_start: 0.7544 (t80) cc_final: 0.6896 (t80) REVERT: A 2961 ILE cc_start: 0.8276 (pt) cc_final: 0.7963 (pt) REVERT: A 2975 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8172 (m-30) REVERT: A 2977 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7698 (ttp-110) REVERT: A 2982 ARG cc_start: 0.8450 (ttp-170) cc_final: 0.8064 (ttm110) REVERT: A 3004 PHE cc_start: 0.6463 (m-10) cc_final: 0.5892 (m-80) REVERT: A 3007 ARG cc_start: 0.7569 (mtt-85) cc_final: 0.7084 (ptp90) REVERT: A 3030 MET cc_start: 0.7121 (mmm) cc_final: 0.6720 (mmm) REVERT: A 3126 MET cc_start: 0.3336 (pmm) cc_final: 0.2958 (pmm) REVERT: A 3176 TYR cc_start: 0.8676 (t80) cc_final: 0.8256 (t80) REVERT: A 3507 CYS cc_start: 0.8518 (m) cc_final: 0.8004 (t) REVERT: A 3552 TYR cc_start: 0.8212 (t80) cc_final: 0.7852 (t80) REVERT: A 3785 GLU cc_start: 0.4822 (OUTLIER) cc_final: 0.4261 (pt0) REVERT: A 3813 PHE cc_start: 0.8317 (m-10) cc_final: 0.8080 (m-10) REVERT: A 3819 LYS cc_start: 0.8912 (ptpt) cc_final: 0.8670 (ptpt) REVERT: A 3859 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9052 (tp) REVERT: A 4001 LEU cc_start: 0.9133 (tp) cc_final: 0.8915 (tt) REVERT: A 4004 MET cc_start: 0.8045 (tpp) cc_final: 0.7693 (tpt) REVERT: A 4042 LEU cc_start: 0.8251 (mp) cc_final: 0.7893 (mp) REVERT: A 4043 MET cc_start: 0.9162 (mmm) cc_final: 0.8939 (mmm) REVERT: A 4128 MET cc_start: 0.7762 (ptp) cc_final: 0.7015 (ptp) REVERT: A 4130 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8940 (mm) REVERT: A 4381 HIS cc_start: 0.5992 (t-90) cc_final: 0.5585 (t-90) outliers start: 80 outliers final: 42 residues processed: 406 average time/residue: 0.3752 time to fit residues: 248.5053 Evaluate side-chains 351 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2975 ASP Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3671 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3804 LEU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3859 ILE Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4130 ILE Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 193 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 240 optimal weight: 20.0000 chunk 278 optimal weight: 0.7980 chunk 53 optimal weight: 0.0670 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2005 GLN A2314 ASN A2377 ASN A2827 HIS A2857 HIS ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS A4397 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.123095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095294 restraints weight = 68526.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.097869 restraints weight = 35378.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099618 restraints weight = 23532.631| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24001 Z= 0.173 Angle : 0.638 14.063 32549 Z= 0.315 Chirality : 0.042 0.316 3651 Planarity : 0.004 0.059 4175 Dihedral : 5.929 120.200 3233 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 3.87 % Allowed : 21.10 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2901 helix: 1.95 (0.13), residues: 1665 sheet: -0.98 (0.32), residues: 258 loop : 0.32 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A2584 HIS 0.007 0.001 HIS A3182 PHE 0.044 0.002 PHE A2635 TYR 0.016 0.001 TYR A2496 ARG 0.007 0.001 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 1359) hydrogen bonds : angle 4.28066 ( 3954) covalent geometry : bond 0.00385 (24001) covalent geometry : angle 0.63794 (32549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 330 time to evaluate : 2.750 Fit side-chains REVERT: A 1657 MET cc_start: 0.6902 (mmm) cc_final: 0.6659 (mmm) REVERT: A 1665 ILE cc_start: 0.8299 (mm) cc_final: 0.8094 (mt) REVERT: A 1691 SER cc_start: 0.5732 (t) cc_final: 0.2962 (m) REVERT: A 1837 GLU cc_start: 0.7920 (tp30) cc_final: 0.7186 (tp30) REVERT: A 1845 TYR cc_start: 0.7748 (m-80) cc_final: 0.7492 (m-80) REVERT: A 2012 MET cc_start: 0.8772 (tmm) cc_final: 0.8437 (tmm) REVERT: A 2263 HIS cc_start: 0.8215 (m90) cc_final: 0.7953 (m90) REVERT: A 2294 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6738 (mp0) REVERT: A 2412 MET cc_start: 0.8182 (mmm) cc_final: 0.7965 (tpt) REVERT: A 2447 MET cc_start: 0.6022 (mtt) cc_final: 0.5566 (mtt) REVERT: A 2481 MET cc_start: 0.7686 (pmm) cc_final: 0.7394 (ttm) REVERT: A 2594 CYS cc_start: 0.7753 (t) cc_final: 0.7312 (t) REVERT: A 2686 MET cc_start: 0.9162 (tpp) cc_final: 0.8905 (tpp) REVERT: A 2841 GLU cc_start: 0.7823 (pm20) cc_final: 0.7498 (pm20) REVERT: A 2851 ASP cc_start: 0.9134 (m-30) cc_final: 0.8586 (m-30) REVERT: A 2867 MET cc_start: 0.7434 (mtt) cc_final: 0.6928 (tpp) REVERT: A 2930 GLN cc_start: 0.6297 (tt0) cc_final: 0.6053 (tm-30) REVERT: A 2959 TYR cc_start: 0.7830 (t80) cc_final: 0.7490 (t80) REVERT: A 2982 ARG cc_start: 0.8444 (ttp-170) cc_final: 0.8100 (ttm110) REVERT: A 3030 MET cc_start: 0.7418 (mmm) cc_final: 0.6796 (mmm) REVERT: A 3126 MET cc_start: 0.3842 (pmm) cc_final: 0.3532 (pmm) REVERT: A 3176 TYR cc_start: 0.8816 (t80) cc_final: 0.8458 (t80) REVERT: A 3507 CYS cc_start: 0.8495 (m) cc_final: 0.7971 (t) REVERT: A 3521 ASP cc_start: 0.8270 (p0) cc_final: 0.7998 (p0) REVERT: A 3785 GLU cc_start: 0.4851 (OUTLIER) cc_final: 0.4271 (pt0) REVERT: A 3813 PHE cc_start: 0.8419 (m-10) cc_final: 0.8169 (m-10) REVERT: A 3819 LYS cc_start: 0.9041 (ptpt) cc_final: 0.8747 (ptpt) REVERT: A 3841 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: A 3859 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9139 (tp) REVERT: A 3906 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7675 (tp-100) REVERT: A 3994 GLN cc_start: 0.8507 (tt0) cc_final: 0.7644 (tm-30) REVERT: A 4004 MET cc_start: 0.8267 (tpp) cc_final: 0.7995 (tpt) REVERT: A 4042 LEU cc_start: 0.8320 (mp) cc_final: 0.8022 (mp) REVERT: A 4043 MET cc_start: 0.9199 (mmm) cc_final: 0.8990 (mmm) REVERT: A 4082 LYS cc_start: 0.7539 (mttt) cc_final: 0.6948 (ptpp) REVERT: A 4092 ARG cc_start: 0.7167 (tpt-90) cc_final: 0.6844 (tpt90) REVERT: A 4128 MET cc_start: 0.7733 (ptp) cc_final: 0.7390 (ptp) REVERT: A 4130 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8984 (mm) REVERT: A 4381 HIS cc_start: 0.5956 (t-90) cc_final: 0.5463 (t-90) REVERT: A 4611 LEU cc_start: 0.9072 (tt) cc_final: 0.8760 (tp) REVERT: A 4617 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8007 (p0) outliers start: 100 outliers final: 55 residues processed: 405 average time/residue: 0.4229 time to fit residues: 282.2423 Evaluate side-chains 355 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 295 time to evaluate : 4.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2993 ILE Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3671 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3841 TYR Chi-restraints excluded: chain A residue 3846 LEU Chi-restraints excluded: chain A residue 3859 ILE Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4130 ILE Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4600 LYS Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 272 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2314 ASN A2414 GLN A2491 GLN A2857 HIS ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS A4397 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.122968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095826 restraints weight = 66743.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.098349 restraints weight = 34108.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.100034 restraints weight = 22547.183| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24001 Z= 0.129 Angle : 0.619 11.723 32549 Z= 0.299 Chirality : 0.041 0.365 3651 Planarity : 0.004 0.042 4175 Dihedral : 5.820 116.578 3233 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 2.86 % Allowed : 22.34 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.16), residues: 2901 helix: 2.00 (0.13), residues: 1665 sheet: -0.87 (0.32), residues: 264 loop : 0.37 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A2584 HIS 0.004 0.001 HIS A3182 PHE 0.045 0.002 PHE A2635 TYR 0.014 0.001 TYR A3103 ARG 0.009 0.000 ARG A2273 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 1359) hydrogen bonds : angle 4.20008 ( 3954) covalent geometry : bond 0.00289 (24001) covalent geometry : angle 0.61869 (32549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 318 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7701 (ptp-110) cc_final: 0.7403 (ptp-170) REVERT: A 1615 LEU cc_start: 0.8362 (tp) cc_final: 0.8081 (pp) REVERT: A 1665 ILE cc_start: 0.8351 (mm) cc_final: 0.8140 (mt) REVERT: A 1837 GLU cc_start: 0.7813 (tp30) cc_final: 0.7374 (tp30) REVERT: A 1845 TYR cc_start: 0.7808 (m-80) cc_final: 0.7533 (m-80) REVERT: A 2012 MET cc_start: 0.8776 (tmm) cc_final: 0.8474 (tmm) REVERT: A 2053 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8129 (mtt) REVERT: A 2084 SER cc_start: 0.8752 (p) cc_final: 0.8505 (t) REVERT: A 2254 ILE cc_start: 0.8555 (mt) cc_final: 0.8200 (pt) REVERT: A 2263 HIS cc_start: 0.8177 (m90) cc_final: 0.7943 (m90) REVERT: A 2294 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6882 (mp0) REVERT: A 2447 MET cc_start: 0.6163 (mtt) cc_final: 0.5433 (mtt) REVERT: A 2481 MET cc_start: 0.7634 (pmm) cc_final: 0.7307 (ttm) REVERT: A 2686 MET cc_start: 0.9071 (tpp) cc_final: 0.8719 (tpp) REVERT: A 2688 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6763 (tm-30) REVERT: A 2712 CYS cc_start: 0.7680 (m) cc_final: 0.7458 (m) REVERT: A 2759 ILE cc_start: 0.5972 (OUTLIER) cc_final: 0.5718 (mm) REVERT: A 2851 ASP cc_start: 0.9119 (m-30) cc_final: 0.8555 (m-30) REVERT: A 2867 MET cc_start: 0.7458 (mtt) cc_final: 0.6961 (tpp) REVERT: A 2961 ILE cc_start: 0.8376 (pt) cc_final: 0.8176 (tt) REVERT: A 2982 ARG cc_start: 0.8463 (ttp-170) cc_final: 0.8086 (ttm110) REVERT: A 3020 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6861 (tp) REVERT: A 3030 MET cc_start: 0.7206 (mmm) cc_final: 0.6709 (mmm) REVERT: A 3126 MET cc_start: 0.3529 (pmm) cc_final: 0.3157 (pmm) REVERT: A 3169 MET cc_start: 0.7571 (mmt) cc_final: 0.7178 (mmt) REVERT: A 3176 TYR cc_start: 0.8758 (t80) cc_final: 0.8370 (t80) REVERT: A 3182 HIS cc_start: 0.9019 (OUTLIER) cc_final: 0.8710 (m90) REVERT: A 3507 CYS cc_start: 0.8410 (m) cc_final: 0.7861 (t) REVERT: A 3521 ASP cc_start: 0.8200 (p0) cc_final: 0.7868 (p0) REVERT: A 3540 ASN cc_start: 0.8145 (m-40) cc_final: 0.7869 (t0) REVERT: A 3785 GLU cc_start: 0.4879 (OUTLIER) cc_final: 0.4276 (pt0) REVERT: A 3813 PHE cc_start: 0.8272 (m-10) cc_final: 0.7968 (m-10) REVERT: A 3819 LYS cc_start: 0.9047 (ptpt) cc_final: 0.8753 (ptpt) REVERT: A 3859 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9049 (tp) REVERT: A 3906 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7671 (tp-100) REVERT: A 3994 GLN cc_start: 0.8450 (tt0) cc_final: 0.7604 (tm-30) REVERT: A 4004 MET cc_start: 0.8259 (tpp) cc_final: 0.7967 (tpt) REVERT: A 4042 LEU cc_start: 0.8235 (mp) cc_final: 0.7980 (mp) REVERT: A 4082 LYS cc_start: 0.7668 (mttt) cc_final: 0.7215 (ptpp) REVERT: A 4128 MET cc_start: 0.7694 (ptp) cc_final: 0.7318 (ptp) REVERT: A 4381 HIS cc_start: 0.5870 (t-90) cc_final: 0.5619 (t-170) REVERT: A 4611 LEU cc_start: 0.9201 (tt) cc_final: 0.8820 (tp) REVERT: A 4617 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8066 (p0) outliers start: 74 outliers final: 38 residues processed: 374 average time/residue: 0.3945 time to fit residues: 242.7772 Evaluate side-chains 330 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3182 HIS Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3671 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3859 ILE Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 49 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 285 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2482 GLN A2689 HIS ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3527 ASN A3535 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4295 GLN A4397 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.116822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088499 restraints weight = 68762.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090995 restraints weight = 35273.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.092688 restraints weight = 23440.239| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24001 Z= 0.217 Angle : 0.710 23.349 32549 Z= 0.349 Chirality : 0.044 0.334 3651 Planarity : 0.005 0.056 4175 Dihedral : 6.075 124.762 3233 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 3.37 % Allowed : 22.42 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.16), residues: 2901 helix: 1.76 (0.13), residues: 1672 sheet: -1.09 (0.31), residues: 278 loop : 0.28 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A2584 HIS 0.006 0.001 HIS A3877 PHE 0.027 0.002 PHE A1551 TYR 0.022 0.002 TYR A1872 ARG 0.010 0.001 ARG A2273 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 1359) hydrogen bonds : angle 4.43778 ( 3954) covalent geometry : bond 0.00494 (24001) covalent geometry : angle 0.71031 (32549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 289 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6628 (mmm) cc_final: 0.6363 (mmm) REVERT: A 1837 GLU cc_start: 0.8011 (tp30) cc_final: 0.7159 (tp30) REVERT: A 1841 GLN cc_start: 0.8426 (mp10) cc_final: 0.8117 (mp10) REVERT: A 1967 MET cc_start: 0.8309 (mmm) cc_final: 0.7951 (mtp) REVERT: A 2263 HIS cc_start: 0.8529 (m90) cc_final: 0.8271 (m90) REVERT: A 2294 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6969 (mp0) REVERT: A 2423 MET cc_start: 0.8844 (mtm) cc_final: 0.8551 (mtm) REVERT: A 2481 MET cc_start: 0.7649 (pmm) cc_final: 0.7181 (ttm) REVERT: A 2535 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 2851 ASP cc_start: 0.9236 (m-30) cc_final: 0.8728 (m-30) REVERT: A 2921 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8424 (mtp85) REVERT: A 2930 GLN cc_start: 0.7176 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 2959 TYR cc_start: 0.7607 (t80) cc_final: 0.7388 (t80) REVERT: A 2982 ARG cc_start: 0.8413 (ttp-170) cc_final: 0.8014 (ttm110) REVERT: A 3007 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.7382 (mtt-85) REVERT: A 3030 MET cc_start: 0.7457 (mmm) cc_final: 0.7162 (mmm) REVERT: A 3126 MET cc_start: 0.4062 (pmm) cc_final: 0.3791 (pmm) REVERT: A 3169 MET cc_start: 0.7604 (mmt) cc_final: 0.7281 (mmt) REVERT: A 3176 TYR cc_start: 0.8975 (t80) cc_final: 0.8590 (t80) REVERT: A 3182 HIS cc_start: 0.9113 (OUTLIER) cc_final: 0.8845 (m90) REVERT: A 3507 CYS cc_start: 0.8576 (m) cc_final: 0.8068 (t) REVERT: A 3640 SER cc_start: 0.8449 (m) cc_final: 0.7970 (p) REVERT: A 3785 GLU cc_start: 0.4632 (OUTLIER) cc_final: 0.3958 (pt0) REVERT: A 3813 PHE cc_start: 0.8454 (m-10) cc_final: 0.8066 (m-10) REVERT: A 3819 LYS cc_start: 0.9176 (ptpt) cc_final: 0.8864 (ptpt) REVERT: A 3841 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: A 3859 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8992 (tp) REVERT: A 3906 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7752 (tp-100) REVERT: A 3994 GLN cc_start: 0.8591 (tt0) cc_final: 0.7989 (tm-30) REVERT: A 4004 MET cc_start: 0.8700 (tpp) cc_final: 0.8437 (tpp) REVERT: A 4043 MET cc_start: 0.9255 (mmm) cc_final: 0.9018 (mmm) REVERT: A 4082 LYS cc_start: 0.7795 (mttt) cc_final: 0.7340 (ptpp) REVERT: A 4128 MET cc_start: 0.7814 (ptp) cc_final: 0.7201 (ptp) REVERT: A 4338 ASP cc_start: 0.7722 (m-30) cc_final: 0.7414 (m-30) REVERT: A 4346 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8583 (mmm) REVERT: A 4381 HIS cc_start: 0.6217 (t-90) cc_final: 0.5875 (t-170) REVERT: A 4426 ASP cc_start: 0.8698 (t0) cc_final: 0.8393 (t0) REVERT: A 4430 ASP cc_start: 0.7579 (m-30) cc_final: 0.7349 (m-30) REVERT: A 4617 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8344 (p0) outliers start: 87 outliers final: 56 residues processed: 351 average time/residue: 0.3496 time to fit residues: 200.9305 Evaluate side-chains 329 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2222 MET Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2921 ARG Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3054 PHE Chi-restraints excluded: chain A residue 3182 HIS Chi-restraints excluded: chain A residue 3186 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3671 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3841 TYR Chi-restraints excluded: chain A residue 3859 ILE Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3987 ILE Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 80 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 245 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2314 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2857 HIS ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3527 ASN A3535 HIS A4063 ASN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.119305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092267 restraints weight = 67569.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.094756 restraints weight = 34127.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.096437 restraints weight = 22445.795| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24001 Z= 0.124 Angle : 0.641 11.186 32549 Z= 0.309 Chirality : 0.042 0.394 3651 Planarity : 0.004 0.042 4175 Dihedral : 5.924 116.637 3233 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 2.28 % Allowed : 23.93 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.16), residues: 2901 helix: 1.94 (0.13), residues: 1673 sheet: -0.92 (0.32), residues: 260 loop : 0.35 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A2584 HIS 0.003 0.001 HIS A3182 PHE 0.053 0.002 PHE A2635 TYR 0.014 0.001 TYR A2496 ARG 0.007 0.000 ARG A2981 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 1359) hydrogen bonds : angle 4.24892 ( 3954) covalent geometry : bond 0.00276 (24001) covalent geometry : angle 0.64104 (32549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7681 (ptp-110) cc_final: 0.7257 (ptp-170) REVERT: A 1837 GLU cc_start: 0.7824 (tp30) cc_final: 0.7282 (tp30) REVERT: A 1967 MET cc_start: 0.8055 (mmm) cc_final: 0.7841 (mtp) REVERT: A 2012 MET cc_start: 0.8737 (tmm) cc_final: 0.8437 (tmm) REVERT: A 2263 HIS cc_start: 0.8340 (m90) cc_final: 0.8113 (m90) REVERT: A 2481 MET cc_start: 0.7544 (pmm) cc_final: 0.7124 (ttm) REVERT: A 2513 GLU cc_start: 0.7715 (tm-30) cc_final: 0.6611 (tm-30) REVERT: A 2799 MET cc_start: 0.8497 (tpp) cc_final: 0.8275 (tpp) REVERT: A 2849 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7871 (m110) REVERT: A 2982 ARG cc_start: 0.8515 (ttp-170) cc_final: 0.8068 (ttm110) REVERT: A 2994 MET cc_start: 0.7955 (mmm) cc_final: 0.7693 (mmm) REVERT: A 3030 MET cc_start: 0.7049 (mmm) cc_final: 0.6668 (mmm) REVERT: A 3169 MET cc_start: 0.7496 (mmt) cc_final: 0.7193 (mmt) REVERT: A 3176 TYR cc_start: 0.8838 (t80) cc_final: 0.8470 (t80) REVERT: A 3507 CYS cc_start: 0.8387 (m) cc_final: 0.7831 (t) REVERT: A 3640 SER cc_start: 0.8430 (m) cc_final: 0.7945 (p) REVERT: A 3720 GLU cc_start: 0.7296 (tp30) cc_final: 0.7048 (tp30) REVERT: A 3785 GLU cc_start: 0.4845 (OUTLIER) cc_final: 0.4122 (pt0) REVERT: A 3813 PHE cc_start: 0.8422 (m-10) cc_final: 0.8063 (m-10) REVERT: A 3859 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8971 (tp) REVERT: A 3906 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7711 (tp-100) REVERT: A 4082 LYS cc_start: 0.7703 (mttt) cc_final: 0.7307 (ptpp) REVERT: A 4262 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8259 (tp40) REVERT: A 4326 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.7696 (p0) REVERT: A 4346 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8676 (mmm) REVERT: A 4381 HIS cc_start: 0.6163 (t-90) cc_final: 0.5586 (t-90) REVERT: A 4426 ASP cc_start: 0.8652 (t0) cc_final: 0.8329 (t0) REVERT: A 4617 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8281 (p0) outliers start: 59 outliers final: 38 residues processed: 352 average time/residue: 0.3545 time to fit residues: 201.4390 Evaluate side-chains 322 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2631 LEU Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2849 ASN Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3859 ILE Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 102 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 157 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 247 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2209 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2677 GLN A2857 HIS ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS A4062 GLN ** A4436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.117971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091412 restraints weight = 68073.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094940 restraints weight = 34774.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094880 restraints weight = 18878.180| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24001 Z= 0.145 Angle : 0.677 13.579 32549 Z= 0.325 Chirality : 0.043 0.391 3651 Planarity : 0.004 0.043 4175 Dihedral : 5.914 117.623 3233 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 2.36 % Allowed : 24.70 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2901 helix: 1.93 (0.13), residues: 1668 sheet: -0.91 (0.32), residues: 266 loop : 0.36 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A2584 HIS 0.004 0.001 HIS A4187 PHE 0.039 0.002 PHE A2751 TYR 0.016 0.001 TYR A1872 ARG 0.014 0.000 ARG A2811 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1359) hydrogen bonds : angle 4.29284 ( 3954) covalent geometry : bond 0.00333 (24001) covalent geometry : angle 0.67707 (32549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 280 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1645 LYS cc_start: 0.8490 (mmtt) cc_final: 0.7878 (ttpt) REVERT: A 1837 GLU cc_start: 0.7811 (tp30) cc_final: 0.7304 (tp30) REVERT: A 1967 MET cc_start: 0.8170 (mmm) cc_final: 0.7935 (mtp) REVERT: A 2012 MET cc_start: 0.8800 (tmm) cc_final: 0.8481 (tmm) REVERT: A 2263 HIS cc_start: 0.8436 (m90) cc_final: 0.8198 (m90) REVERT: A 2423 MET cc_start: 0.8863 (mtm) cc_final: 0.8570 (mtm) REVERT: A 2481 MET cc_start: 0.7554 (pmm) cc_final: 0.7148 (ttm) REVERT: A 2513 GLU cc_start: 0.7810 (tm-30) cc_final: 0.6695 (tm-30) REVERT: A 2849 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7622 (m110) REVERT: A 2930 GLN cc_start: 0.7195 (tm-30) cc_final: 0.6926 (tm-30) REVERT: A 2982 ARG cc_start: 0.8551 (ttp-170) cc_final: 0.8059 (ttm110) REVERT: A 3030 MET cc_start: 0.7300 (mmm) cc_final: 0.6691 (mmm) REVERT: A 3126 MET cc_start: 0.4793 (pmm) cc_final: 0.4402 (pmm) REVERT: A 3169 MET cc_start: 0.7694 (mmt) cc_final: 0.7358 (mmt) REVERT: A 3176 TYR cc_start: 0.8890 (t80) cc_final: 0.8462 (t80) REVERT: A 3507 CYS cc_start: 0.8430 (m) cc_final: 0.7856 (t) REVERT: A 3640 SER cc_start: 0.8350 (m) cc_final: 0.7908 (p) REVERT: A 3720 GLU cc_start: 0.7417 (tp30) cc_final: 0.7072 (tp30) REVERT: A 3785 GLU cc_start: 0.4673 (OUTLIER) cc_final: 0.3979 (pt0) REVERT: A 3813 PHE cc_start: 0.8440 (m-10) cc_final: 0.8062 (m-10) REVERT: A 3859 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9001 (tp) REVERT: A 3906 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7757 (tp-100) REVERT: A 4082 LYS cc_start: 0.7894 (mttt) cc_final: 0.7417 (ptpp) REVERT: A 4346 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8743 (mmm) REVERT: A 4381 HIS cc_start: 0.6230 (t-90) cc_final: 0.5821 (t-90) REVERT: A 4617 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8324 (p0) outliers start: 61 outliers final: 42 residues processed: 326 average time/residue: 0.3438 time to fit residues: 184.2096 Evaluate side-chains 312 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1916 VAL Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2631 LEU Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2849 ASN Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3671 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3859 ILE Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 247 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 279 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 226 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN A1961 ASN A2299 GLN A2314 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3535 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.119514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.091423 restraints weight = 67764.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093992 restraints weight = 34154.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.095711 restraints weight = 22460.468| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24001 Z= 0.122 Angle : 0.667 12.664 32549 Z= 0.320 Chirality : 0.042 0.390 3651 Planarity : 0.004 0.051 4175 Dihedral : 5.814 112.268 3233 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Rotamer: Outliers : 1.66 % Allowed : 25.40 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.16), residues: 2901 helix: 1.97 (0.13), residues: 1669 sheet: -0.83 (0.33), residues: 256 loop : 0.35 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A3093 HIS 0.003 0.001 HIS A2577 PHE 0.039 0.001 PHE A2751 TYR 0.014 0.001 TYR A3026 ARG 0.011 0.000 ARG A2811 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 1359) hydrogen bonds : angle 4.24069 ( 3954) covalent geometry : bond 0.00272 (24001) covalent geometry : angle 0.66670 (32549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7744 (ptp-110) cc_final: 0.7342 (ptp-170) REVERT: A 1645 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7810 (ttpt) REVERT: A 1837 GLU cc_start: 0.7848 (tp30) cc_final: 0.7335 (tp30) REVERT: A 2012 MET cc_start: 0.8740 (tmm) cc_final: 0.8423 (tmm) REVERT: A 2263 HIS cc_start: 0.8358 (m90) cc_final: 0.8148 (m90) REVERT: A 2423 MET cc_start: 0.8795 (mtm) cc_final: 0.8483 (mtm) REVERT: A 2447 MET cc_start: 0.6547 (mmt) cc_final: 0.6297 (tpp) REVERT: A 2481 MET cc_start: 0.7484 (pmm) cc_final: 0.7094 (ttm) REVERT: A 2513 GLU cc_start: 0.7849 (tm-30) cc_final: 0.6751 (tm-30) REVERT: A 2930 GLN cc_start: 0.7109 (tm-30) cc_final: 0.6780 (tm-30) REVERT: A 2961 ILE cc_start: 0.8676 (pt) cc_final: 0.8323 (tt) REVERT: A 2982 ARG cc_start: 0.8542 (ttp-170) cc_final: 0.8032 (ttm110) REVERT: A 3030 MET cc_start: 0.7277 (mmm) cc_final: 0.6671 (mmm) REVERT: A 3126 MET cc_start: 0.4696 (pmm) cc_final: 0.4492 (pmm) REVERT: A 3169 MET cc_start: 0.7642 (mmt) cc_final: 0.7326 (mmt) REVERT: A 3176 TYR cc_start: 0.8826 (t80) cc_final: 0.8407 (t80) REVERT: A 3507 CYS cc_start: 0.8391 (m) cc_final: 0.7831 (t) REVERT: A 3640 SER cc_start: 0.8314 (m) cc_final: 0.7879 (p) REVERT: A 3785 GLU cc_start: 0.4639 (OUTLIER) cc_final: 0.3962 (pt0) REVERT: A 3813 PHE cc_start: 0.8457 (m-10) cc_final: 0.8079 (m-10) REVERT: A 3859 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8978 (tp) REVERT: A 3906 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7761 (tp-100) REVERT: A 4082 LYS cc_start: 0.7870 (mttt) cc_final: 0.7405 (ptpp) REVERT: A 4262 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8195 (tp40) REVERT: A 4346 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8686 (mmm) REVERT: A 4381 HIS cc_start: 0.6081 (t-90) cc_final: 0.5450 (t-90) REVERT: A 4617 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8315 (p0) outliers start: 43 outliers final: 34 residues processed: 328 average time/residue: 0.3808 time to fit residues: 206.3039 Evaluate side-chains 312 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1916 VAL Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2082 SER Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2624 SER Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3671 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3859 ILE Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 281 optimal weight: 0.2980 chunk 201 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 252 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2314 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4436 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 = 0.3956 r_free = 0.3956 target = 0.118861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090425 restraints weight = 67850.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.092986 restraints weight = 34707.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094704 restraints weight = 22929.733| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24001 Z= 0.129 Angle : 0.664 12.466 32549 Z= 0.320 Chirality : 0.043 0.390 3651 Planarity : 0.004 0.050 4175 Dihedral : 5.770 111.380 3233 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.38 % Rotamer: Outliers : 1.94 % Allowed : 25.40 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.16), residues: 2901 helix: 1.98 (0.13), residues: 1665 sheet: -0.95 (0.33), residues: 248 loop : 0.34 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.002 TRP A3093 HIS 0.004 0.001 HIS A4187 PHE 0.038 0.002 PHE A2751 TYR 0.015 0.001 TYR A1872 ARG 0.011 0.000 ARG A2811 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 1359) hydrogen bonds : angle 4.23026 ( 3954) covalent geometry : bond 0.00295 (24001) covalent geometry : angle 0.66375 (32549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10133.96 seconds wall clock time: 178 minutes 20.02 seconds (10700.02 seconds total)