Starting phenix.real_space_refine on Fri Sep 19 06:43:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bn0_44717/09_2025/9bn0_44717.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bn0_44717/09_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_44717/09_2025/9bn0_44717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bn0_44717/09_2025/9bn0_44717.map" model { file = "/net/cci-nas-00/data/ceres_data/9bn0_44717/09_2025/9bn0_44717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bn0_44717/09_2025/9bn0_44717.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.47, per 1000 atoms: 0.23 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: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.53 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: 7.15 Time building geometry restraints manager: 2.77 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: 1.200 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.790 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (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 ARG 0.007 0.000 ARG A3910 TYR 0.027 0.001 TYR A1546 PHE 0.021 0.001 PHE A1938 TRP 0.038 0.001 TRP A1523 HIS 0.006 0.001 HIS A3155 Details of bonding type rmsd covalent geometry : bond 0.00476 (24001) covalent geometry : angle 0.71751 (32549) hydrogen bonds : bond 0.13610 ( 1359) hydrogen bonds : angle 5.59690 ( 3954) *********************** 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 : 0.909 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: 0.8371 (tp) REVERT: A 2666 ILE cc_start: 0.7135 (mm) cc_final: 0.6455 (mt) REVERT: A 3171 ILE cc_start: 0.7435 (mm) cc_final: 0.7145 (mt) REVERT: A 3584 ASN cc_start: 0.5407 (m-40) cc_final: 0.5031 (m-40) REVERT: A 3815 MET cc_start: 0.6789 (mtm) cc_final: 0.6478 (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: 0.1838 time to fit residues: 212.9033 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 : 0.933 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0030 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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** A2329 ASN 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 A4062 GLN A4085 ASN ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4137 ASN A4397 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.134685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.108247 restraints weight = 67286.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.111032 restraints weight = 34590.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.112944 restraints weight = 22538.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.114134 restraints weight = 17141.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.114926 restraints weight = 14457.056| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24001 Z= 0.154 Angle : 0.674 15.483 32549 Z= 0.331 Chirality : 0.041 0.183 3651 Planarity : 0.004 0.056 4175 Dihedral : 6.181 120.099 3236 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.72 % Rotamer: Outliers : 2.75 % Allowed : 21.99 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.16), residues: 2901 helix: 1.98 (0.13), residues: 1672 sheet: -0.96 (0.32), residues: 255 loop : 0.22 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2843 TYR 0.021 0.002 TYR A3103 PHE 0.031 0.002 PHE A2751 TRP 0.024 0.002 TRP A2802 HIS 0.010 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00340 (24001) covalent geometry : angle 0.67420 (32549) hydrogen bonds : bond 0.04479 ( 1359) hydrogen bonds : angle 4.58011 ( 3954) *********************** 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 481 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 410 time to evaluate : 0.974 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 1542 ARG cc_start: 0.7663 (ptp-110) cc_final: 0.7267 (ptp-170) REVERT: A 1814 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 1841 GLN cc_start: 0.8054 (mp10) cc_final: 0.7439 (mp10) REVERT: A 1861 MET cc_start: 0.7799 (ttt) cc_final: 0.7499 (ttt) REVERT: A 1967 MET cc_start: 0.7583 (mtp) cc_final: 0.7281 (ttt) REVERT: A 2012 MET cc_start: 0.8747 (tmm) cc_final: 0.8474 (tmm) REVERT: A 2069 ILE cc_start: 0.9166 (tp) cc_final: 0.8825 (tp) REVERT: A 2481 MET cc_start: 0.7703 (pmm) cc_final: 0.7370 (ttm) REVERT: A 2759 ILE cc_start: 0.5858 (OUTLIER) cc_final: 0.5433 (mm) REVERT: A 2806 ILE cc_start: 0.7735 (mm) cc_final: 0.7349 (mm) REVERT: A 2825 TRP cc_start: 0.6613 (t60) cc_final: 0.6408 (t60) REVERT: A 2851 ASP cc_start: 0.8969 (m-30) cc_final: 0.8383 (m-30) REVERT: A 2867 MET cc_start: 0.6973 (mtt) cc_final: 0.6396 (tpt) REVERT: A 2961 ILE cc_start: 0.8317 (pt) cc_final: 0.7708 (pt) REVERT: A 3706 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8316 (m) REVERT: A 3819 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8492 (ptpt) REVERT: A 3882 THR cc_start: 0.9233 (m) cc_final: 0.8969 (p) REVERT: A 4008 PHE cc_start: 0.8563 (t80) cc_final: 0.8118 (t80) REVERT: A 4043 MET cc_start: 0.9088 (mmm) cc_final: 0.8831 (mmm) REVERT: A 4079 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7510 (mm-40) REVERT: A 4082 LYS cc_start: 0.7451 (mttt) cc_final: 0.6953 (ptpp) REVERT: A 4116 LEU cc_start: 0.7041 (mt) cc_final: 0.6654 (mp) REVERT: A 4381 HIS cc_start: 0.5788 (t-90) cc_final: 0.5476 (t-170) outliers start: 71 outliers final: 27 residues processed: 462 average time/residue: 0.1523 time to fit residues: 110.1336 Evaluate side-chains 359 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 330 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 1676 ILE Chi-restraints excluded: chain A residue 1812 ILE 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 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 185 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 221 optimal weight: 0.3980 chunk 147 optimal weight: 0.0770 chunk 88 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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** A2677 GLN A2752 ASN A2857 HIS A3047 HIS A3063 HIS ** A3700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4085 ASN A4397 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.131249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.104619 restraints weight = 67221.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.107217 restraints weight = 34510.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.109016 restraints weight = 22615.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.110194 restraints weight = 17302.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.110826 restraints weight = 14631.127| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24001 Z= 0.136 Angle : 0.620 11.792 32549 Z= 0.302 Chirality : 0.041 0.283 3651 Planarity : 0.004 0.047 4175 Dihedral : 6.008 118.154 3234 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 2.94 % Allowed : 21.33 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.16), residues: 2901 helix: 2.05 (0.13), residues: 1659 sheet: -1.05 (0.31), residues: 266 loop : 0.36 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2273 TYR 0.017 0.001 TYR A3103 PHE 0.026 0.002 PHE A3832 TRP 0.023 0.002 TRP A2584 HIS 0.018 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00308 (24001) covalent geometry : angle 0.62025 (32549) hydrogen bonds : bond 0.03987 ( 1359) hydrogen bonds : angle 4.37665 ( 3954) *********************** 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 443 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 367 time to evaluate : 0.833 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 1615 LEU cc_start: 0.8518 (tp) cc_final: 0.8284 (pp) REVERT: A 1841 GLN cc_start: 0.8278 (mp10) cc_final: 0.7769 (mp10) REVERT: A 1861 MET cc_start: 0.7838 (ttt) cc_final: 0.7411 (ttt) REVERT: A 2069 ILE cc_start: 0.9158 (tp) cc_final: 0.8877 (tp) REVERT: A 2294 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6706 (mp0) REVERT: A 2481 MET cc_start: 0.7770 (pmm) cc_final: 0.7463 (ttm) REVERT: A 2591 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 2594 CYS cc_start: 0.7341 (t) cc_final: 0.7042 (t) REVERT: A 2759 ILE cc_start: 0.5741 (OUTLIER) cc_final: 0.5310 (mm) REVERT: A 2851 ASP cc_start: 0.9026 (m-30) cc_final: 0.8485 (m-30) REVERT: A 2867 MET cc_start: 0.7082 (mtt) cc_final: 0.6562 (tpt) REVERT: A 2961 ILE cc_start: 0.8301 (pt) cc_final: 0.7908 (pt) REVERT: A 2975 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: A 3016 GLU cc_start: 0.7449 (pp20) cc_final: 0.7170 (tm-30) REVERT: A 3030 MET cc_start: 0.6947 (mmm) cc_final: 0.6604 (mmm) REVERT: A 3126 MET cc_start: 0.3102 (pmm) cc_final: 0.2729 (pmm) REVERT: A 3176 TYR cc_start: 0.8615 (t80) cc_final: 0.8278 (t80) REVERT: A 3507 CYS cc_start: 0.8673 (m) cc_final: 0.8060 (t) REVERT: A 3552 TYR cc_start: 0.8116 (t80) cc_final: 0.7649 (t80) REVERT: A 3813 PHE cc_start: 0.8527 (m-10) cc_final: 0.8092 (m-10) REVERT: A 3819 LYS cc_start: 0.8826 (ptpt) cc_final: 0.8508 (ptpt) REVERT: A 3830 GLN cc_start: 0.8887 (tp40) cc_final: 0.8019 (tp40) REVERT: A 3834 ASP cc_start: 0.8004 (m-30) cc_final: 0.6993 (m-30) REVERT: A 4004 MET cc_start: 0.7761 (tpp) cc_final: 0.7290 (tpt) REVERT: A 4008 PHE cc_start: 0.8639 (t80) cc_final: 0.8006 (t80) REVERT: A 4043 MET cc_start: 0.9132 (mmm) cc_final: 0.8911 (mmm) REVERT: A 4128 MET cc_start: 0.7783 (ptp) cc_final: 0.7505 (ptp) REVERT: A 4158 LEU cc_start: 0.9358 (mt) cc_final: 0.9155 (mt) REVERT: A 4381 HIS cc_start: 0.5909 (t-90) cc_final: 0.5484 (t-90) REVERT: A 4429 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7819 (mm-40) outliers start: 76 outliers final: 37 residues processed: 423 average time/residue: 0.1480 time to fit residues: 101.3885 Evaluate side-chains 358 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1563 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 1791 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1882 THR 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 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 2591 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 2975 ASP Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3201 LEU 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 3846 LEU Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 3987 ILE 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 4600 LYS 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 238 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 86 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 A2271 ASN A2442 GLN A2827 HIS A2857 HIS A3584 ASN A4397 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.130582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.103364 restraints weight = 68715.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.106083 restraints weight = 35082.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.107933 restraints weight = 22928.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.109109 restraints weight = 17538.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.109839 restraints weight = 14867.536| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4141 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= 0.127 Angle : 0.610 11.765 32549 Z= 0.294 Chirality : 0.040 0.331 3651 Planarity : 0.004 0.044 4175 Dihedral : 5.892 115.246 3234 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 2.59 % Allowed : 21.91 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.16), residues: 2901 helix: 2.04 (0.13), residues: 1666 sheet: -0.94 (0.32), residues: 264 loop : 0.33 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A4092 TYR 0.023 0.001 TYR A2777 PHE 0.027 0.002 PHE A4613 TRP 0.040 0.002 TRP A2584 HIS 0.004 0.001 HIS A2730 Details of bonding type rmsd covalent geometry : bond 0.00286 (24001) covalent geometry : angle 0.61017 (32549) hydrogen bonds : bond 0.03832 ( 1359) hydrogen bonds : angle 4.25374 ( 3954) *********************** 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 419 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 352 time to evaluate : 0.841 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 1615 LEU cc_start: 0.8531 (tp) cc_final: 0.8252 (pp) REVERT: A 1657 MET cc_start: 0.6831 (mmm) cc_final: 0.6618 (mmm) REVERT: A 1665 ILE cc_start: 0.8029 (mm) cc_final: 0.7702 (mt) REVERT: A 1841 GLN cc_start: 0.8381 (mp10) cc_final: 0.7902 (mp10) REVERT: A 1861 MET cc_start: 0.7917 (ttt) cc_final: 0.7486 (ttt) REVERT: A 2012 MET cc_start: 0.8832 (tmm) cc_final: 0.8533 (tmm) REVERT: A 2069 ILE cc_start: 0.9124 (tp) cc_final: 0.8862 (tp) REVERT: A 2294 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6711 (mp0) REVERT: A 2481 MET cc_start: 0.7774 (pmm) cc_final: 0.7328 (ttm) REVERT: A 2594 CYS cc_start: 0.7507 (t) cc_final: 0.7174 (t) REVERT: A 2759 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5409 (mm) REVERT: A 2779 MET cc_start: 0.8348 (tpp) cc_final: 0.8081 (ptm) REVERT: A 2825 TRP cc_start: 0.6771 (t60) cc_final: 0.6537 (t60) REVERT: A 2851 ASP cc_start: 0.9051 (m-30) cc_final: 0.8495 (m-30) REVERT: A 2867 MET cc_start: 0.7303 (mtt) cc_final: 0.6819 (tpt) REVERT: A 2959 TYR cc_start: 0.7393 (t80) cc_final: 0.7066 (t80) REVERT: A 2982 ARG cc_start: 0.8475 (ttp-170) cc_final: 0.8092 (ttm110) REVERT: A 3007 ARG cc_start: 0.7605 (mtt-85) cc_final: 0.7384 (mtt-85) REVERT: A 3016 GLU cc_start: 0.7496 (pp20) cc_final: 0.7263 (tm-30) REVERT: A 3030 MET cc_start: 0.7259 (mmm) cc_final: 0.6585 (mmm) REVERT: A 3126 MET cc_start: 0.3199 (pmm) cc_final: 0.2807 (pmm) REVERT: A 3176 TYR cc_start: 0.8662 (t80) cc_final: 0.8328 (t80) REVERT: A 3507 CYS cc_start: 0.8677 (m) cc_final: 0.8010 (t) REVERT: A 3552 TYR cc_start: 0.8163 (t80) cc_final: 0.7929 (t80) REVERT: A 3785 GLU cc_start: 0.4820 (OUTLIER) cc_final: 0.4284 (pt0) REVERT: A 3813 PHE cc_start: 0.8527 (m-10) cc_final: 0.8102 (m-10) REVERT: A 3819 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8524 (ptpt) REVERT: A 3830 GLN cc_start: 0.9031 (tp40) cc_final: 0.8205 (tp-100) REVERT: A 3833 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8470 (mm) REVERT: A 3834 ASP cc_start: 0.8040 (m-30) cc_final: 0.7033 (m-30) REVERT: A 4004 MET cc_start: 0.7838 (tpp) cc_final: 0.7417 (tpt) REVERT: A 4008 PHE cc_start: 0.8691 (t80) cc_final: 0.7987 (t80) REVERT: A 4043 MET cc_start: 0.9240 (mmm) cc_final: 0.8928 (mmm) REVERT: A 4381 HIS cc_start: 0.5933 (t-90) cc_final: 0.5494 (t-90) outliers start: 67 outliers final: 38 residues processed: 399 average time/residue: 0.1508 time to fit residues: 97.4399 Evaluate side-chains 360 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 319 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1941 MET 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 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 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 2759 ILE Chi-restraints excluded: chain A residue 2873 TYR Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3584 ASN Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3638 VAL 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 3833 LEU Chi-restraints excluded: chain A residue 3846 LEU 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 4189 ILE Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4454 GLU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 225 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 67 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** A2209 GLN A2677 GLN A2857 HIS ** A4131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4397 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.128288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.100800 restraints weight = 68014.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.103474 restraints weight = 35085.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.105274 restraints weight = 23246.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.106426 restraints weight = 17910.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.107009 restraints weight = 15249.078| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4480 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= 0.133 Angle : 0.603 13.265 32549 Z= 0.291 Chirality : 0.040 0.177 3651 Planarity : 0.004 0.050 4175 Dihedral : 5.817 115.033 3233 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % Rotamer: Outliers : 2.75 % Allowed : 22.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.16), residues: 2901 helix: 2.05 (0.13), residues: 1669 sheet: -0.92 (0.32), residues: 265 loop : 0.37 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1485 TYR 0.015 0.001 TYR A2496 PHE 0.020 0.001 PHE A4017 TRP 0.058 0.002 TRP A2584 HIS 0.005 0.001 HIS A2730 Details of bonding type rmsd covalent geometry : bond 0.00302 (24001) covalent geometry : angle 0.60309 (32549) hydrogen bonds : bond 0.03695 ( 1359) hydrogen bonds : angle 4.19317 ( 3954) *********************** 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 413 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 342 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1615 LEU cc_start: 0.8534 (tp) cc_final: 0.8251 (pp) REVERT: A 1661 VAL cc_start: 0.7160 (t) cc_final: 0.6935 (t) REVERT: A 1665 ILE cc_start: 0.8121 (mm) cc_final: 0.7849 (mt) REVERT: A 1841 GLN cc_start: 0.8439 (mp10) cc_final: 0.7982 (mp10) REVERT: A 1861 MET cc_start: 0.7952 (ttt) cc_final: 0.7556 (ttt) REVERT: A 2012 MET cc_start: 0.8799 (tmm) cc_final: 0.8484 (tmm) REVERT: A 2069 ILE cc_start: 0.9126 (tp) cc_final: 0.8881 (tp) REVERT: A 2294 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6641 (mp0) REVERT: A 2481 MET cc_start: 0.7761 (pmm) cc_final: 0.7421 (ttm) REVERT: A 2594 CYS cc_start: 0.7534 (t) cc_final: 0.7023 (t) REVERT: A 2759 ILE cc_start: 0.5817 (OUTLIER) cc_final: 0.5493 (mm) REVERT: A 2779 MET cc_start: 0.8484 (tpp) cc_final: 0.8273 (ptm) REVERT: A 2851 ASP cc_start: 0.8996 (m-30) cc_final: 0.8427 (m-30) REVERT: A 2867 MET cc_start: 0.7285 (mtt) cc_final: 0.6861 (tpt) REVERT: A 2873 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.3973 (t80) REVERT: A 2959 TYR cc_start: 0.7625 (t80) cc_final: 0.7321 (t80) REVERT: A 2982 ARG cc_start: 0.8492 (ttp-170) cc_final: 0.8131 (ttm110) REVERT: A 3007 ARG cc_start: 0.7733 (mtt-85) cc_final: 0.7471 (mtt-85) REVERT: A 3030 MET cc_start: 0.7302 (mmm) cc_final: 0.6661 (mmm) REVERT: A 3126 MET cc_start: 0.3105 (pmm) cc_final: 0.2693 (pmm) REVERT: A 3176 TYR cc_start: 0.8672 (t80) cc_final: 0.8244 (t80) REVERT: A 3193 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 3507 CYS cc_start: 0.8523 (m) cc_final: 0.7950 (t) REVERT: A 3552 TYR cc_start: 0.8211 (t80) cc_final: 0.7999 (t80) REVERT: A 3765 THR cc_start: -0.6124 (OUTLIER) cc_final: -0.6389 (p) REVERT: A 3785 GLU cc_start: 0.4826 (OUTLIER) cc_final: 0.4274 (pt0) REVERT: A 3813 PHE cc_start: 0.8389 (m-10) cc_final: 0.8139 (m-10) REVERT: A 3819 LYS cc_start: 0.8905 (ptpt) cc_final: 0.8647 (ptpt) REVERT: A 3830 GLN cc_start: 0.8954 (tp40) cc_final: 0.8037 (tp-100) REVERT: A 3834 ASP cc_start: 0.8008 (m-30) cc_final: 0.6932 (m-30) REVERT: A 4004 MET cc_start: 0.7981 (tpp) cc_final: 0.7581 (tpt) REVERT: A 4008 PHE cc_start: 0.8633 (t80) cc_final: 0.7972 (t80) REVERT: A 4043 MET cc_start: 0.9217 (mmm) cc_final: 0.8960 (mmm) REVERT: A 4079 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7587 (mm-40) REVERT: A 4082 LYS cc_start: 0.7645 (mttt) cc_final: 0.7099 (ptpp) REVERT: A 4381 HIS cc_start: 0.5970 (t-90) cc_final: 0.5551 (t-90) outliers start: 71 outliers final: 43 residues processed: 395 average time/residue: 0.1377 time to fit residues: 89.0169 Evaluate side-chains 348 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 1676 ILE 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 2355 THR Chi-restraints excluded: chain A residue 2448 ASP 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 2759 ILE Chi-restraints excluded: chain A residue 2873 TYR Chi-restraints excluded: chain A residue 2946 LEU 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 3638 VAL Chi-restraints excluded: chain A residue 3671 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 3772 ASN 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 3938 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4246 LEU 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 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 191 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2314 ASN A2377 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2442 GLN A2482 GLN ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 ASN A3527 ASN A3535 HIS A4397 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.121492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.093931 restraints weight = 67707.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096351 restraints weight = 34809.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.098035 restraints weight = 23275.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.098973 restraints weight = 18063.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099749 restraints weight = 15629.044| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24001 Z= 0.201 Angle : 0.684 19.774 32549 Z= 0.337 Chirality : 0.043 0.216 3651 Planarity : 0.005 0.062 4175 Dihedral : 6.021 121.350 3233 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 3.68 % Allowed : 21.99 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.16), residues: 2901 helix: 1.92 (0.13), residues: 1671 sheet: -0.96 (0.31), residues: 264 loop : 0.28 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1485 TYR 0.019 0.002 TYR A3641 PHE 0.031 0.002 PHE A2992 TRP 0.087 0.002 TRP A2584 HIS 0.006 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00451 (24001) covalent geometry : angle 0.68410 (32549) hydrogen bonds : bond 0.04052 ( 1359) hydrogen bonds : angle 4.35760 ( 3954) *********************** 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 418 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 323 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1691 SER cc_start: 0.5586 (t) cc_final: 0.2799 (m) REVERT: A 1837 GLU cc_start: 0.7871 (tp30) cc_final: 0.7084 (tp30) REVERT: A 2273 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7245 (tmm160) REVERT: A 2294 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6728 (mp0) REVERT: A 2447 MET cc_start: 0.6416 (mtt) cc_final: 0.5897 (mtt) REVERT: A 2481 MET cc_start: 0.7515 (pmm) cc_final: 0.7293 (ttm) REVERT: A 2841 GLU cc_start: 0.7810 (pm20) cc_final: 0.7335 (pm20) REVERT: A 2851 ASP cc_start: 0.9112 (m-30) cc_final: 0.8599 (m-30) REVERT: A 2867 MET cc_start: 0.7441 (mtt) cc_final: 0.6980 (tpp) REVERT: A 2873 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.4462 (t80) REVERT: A 2959 TYR cc_start: 0.7999 (t80) cc_final: 0.7739 (t80) REVERT: A 3007 ARG cc_start: 0.7847 (mtt-85) cc_final: 0.7540 (mtt-85) REVERT: A 3030 MET cc_start: 0.7216 (mmm) cc_final: 0.6447 (mmm) REVERT: A 3126 MET cc_start: 0.3478 (pmm) cc_final: 0.3206 (pmm) REVERT: A 3507 CYS cc_start: 0.8499 (m) cc_final: 0.8030 (t) REVERT: A 3521 ASP cc_start: 0.8191 (p0) cc_final: 0.7899 (p0) REVERT: A 3640 SER cc_start: 0.8700 (m) cc_final: 0.8092 (p) REVERT: A 3785 GLU cc_start: 0.4884 (OUTLIER) cc_final: 0.4253 (pt0) REVERT: A 3813 PHE cc_start: 0.8449 (m-10) cc_final: 0.8163 (m-10) REVERT: A 3819 LYS cc_start: 0.9070 (ptpt) cc_final: 0.8757 (ptpt) REVERT: A 3830 GLN cc_start: 0.8977 (tp40) cc_final: 0.8531 (tp-100) REVERT: A 3906 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7669 (tp-100) REVERT: A 4004 MET cc_start: 0.8383 (tpp) cc_final: 0.8098 (tpt) REVERT: A 4043 MET cc_start: 0.9254 (mmm) cc_final: 0.9047 (mmm) REVERT: A 4381 HIS cc_start: 0.5898 (t-90) cc_final: 0.5695 (t-170) REVERT: A 4454 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: A 4617 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8143 (p0) outliers start: 95 outliers final: 48 residues processed: 393 average time/residue: 0.1440 time to fit residues: 91.6061 Evaluate side-chains 346 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 1672 VAL Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1684 VAL 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 2222 MET Chi-restraints excluded: chain A residue 2355 THR 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 2466 CYS 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 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 2734 VAL Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2873 TYR Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2980 LEU Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3172 THR 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 3846 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4246 LEU 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 146 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 125 optimal weight: 0.4980 chunk 263 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 142 optimal weight: 0.0470 chunk 235 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 255 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1961 ASN A2414 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2857 HIS A3014 ASN A3527 ASN A3535 HIS A3542 GLN A4062 GLN A4397 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.123796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.096375 restraints weight = 68267.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.098957 restraints weight = 34892.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.100684 restraints weight = 23029.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.101645 restraints weight = 17843.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.102462 restraints weight = 15370.469| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24001 Z= 0.122 Angle : 0.634 12.118 32549 Z= 0.307 Chirality : 0.041 0.239 3651 Planarity : 0.004 0.053 4175 Dihedral : 5.857 115.048 3233 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 2.17 % Allowed : 23.58 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.16), residues: 2901 helix: 2.01 (0.13), residues: 1670 sheet: -0.83 (0.32), residues: 257 loop : 0.36 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1485 TYR 0.015 0.001 TYR A2193 PHE 0.047 0.002 PHE A2635 TRP 0.065 0.002 TRP A2584 HIS 0.004 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00273 (24001) covalent geometry : angle 0.63450 (32549) hydrogen bonds : bond 0.03726 ( 1359) hydrogen bonds : angle 4.20364 ( 3954) *********************** 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 383 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 327 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1837 GLU cc_start: 0.7798 (tp30) cc_final: 0.7315 (tp30) REVERT: A 1967 MET cc_start: 0.8015 (mmm) cc_final: 0.7506 (mtp) REVERT: A 2012 MET cc_start: 0.8745 (tmm) cc_final: 0.8439 (tmm) REVERT: A 2053 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8103 (mtt) REVERT: A 2084 SER cc_start: 0.8704 (p) cc_final: 0.8462 (t) REVERT: A 2294 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6967 (mp0) REVERT: A 2447 MET cc_start: 0.6291 (mtt) cc_final: 0.5810 (mtt) REVERT: A 2513 GLU cc_start: 0.7788 (tm-30) cc_final: 0.6871 (tm-30) REVERT: A 2537 TYR cc_start: 0.7555 (m-10) cc_final: 0.7167 (m-10) REVERT: A 2712 CYS cc_start: 0.7692 (m) cc_final: 0.7322 (m) REVERT: A 2799 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8396 (tpp) REVERT: A 2851 ASP cc_start: 0.9056 (m-30) cc_final: 0.8508 (m-30) REVERT: A 2867 MET cc_start: 0.7416 (mtt) cc_final: 0.6946 (tpp) REVERT: A 2873 TYR cc_start: 0.6504 (OUTLIER) cc_final: 0.4226 (t80) REVERT: A 2921 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7765 (mtt90) REVERT: A 2961 ILE cc_start: 0.8437 (tt) cc_final: 0.8105 (pt) REVERT: A 3007 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7541 (mtt-85) REVERT: A 3030 MET cc_start: 0.7346 (mmm) cc_final: 0.6486 (mmm) REVERT: A 3062 LEU cc_start: 0.8506 (tp) cc_final: 0.8267 (tp) REVERT: A 3126 MET cc_start: 0.3942 (pmm) cc_final: 0.3701 (pmm) REVERT: A 3169 MET cc_start: 0.7763 (mmt) cc_final: 0.7381 (mmt) REVERT: A 3507 CYS cc_start: 0.8380 (m) cc_final: 0.7853 (t) REVERT: A 3640 SER cc_start: 0.8389 (m) cc_final: 0.7941 (p) REVERT: A 3785 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4272 (pt0) REVERT: A 3813 PHE cc_start: 0.8303 (m-10) cc_final: 0.8015 (m-10) REVERT: A 3819 LYS cc_start: 0.9043 (ptpt) cc_final: 0.8740 (ptpt) REVERT: A 3830 GLN cc_start: 0.8898 (tp40) cc_final: 0.8645 (tp40) REVERT: A 3906 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7642 (tp-100) REVERT: A 3994 GLN cc_start: 0.8404 (tt0) cc_final: 0.7633 (tm-30) REVERT: A 4008 PHE cc_start: 0.8948 (t80) cc_final: 0.8678 (t80) REVERT: A 4128 MET cc_start: 0.8329 (pmm) cc_final: 0.7231 (ptp) REVERT: A 4346 MET cc_start: 0.8804 (mmt) cc_final: 0.8316 (mmm) REVERT: A 4426 ASP cc_start: 0.8568 (t0) cc_final: 0.8094 (t0) REVERT: A 4430 ASP cc_start: 0.7340 (m-30) cc_final: 0.7077 (m-30) REVERT: A 4611 LEU cc_start: 0.9070 (tt) cc_final: 0.8770 (tp) REVERT: A 4617 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8035 (p0) outliers start: 56 outliers final: 34 residues processed: 369 average time/residue: 0.1626 time to fit residues: 96.8195 Evaluate side-chains 334 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 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 2574 THR Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2620 LEU 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 2799 MET Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2873 TYR Chi-restraints excluded: chain A residue 2921 ARG 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 3772 ASN Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3987 ILE Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4246 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 255 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2689 HIS ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3063 HIS A3527 ASN A3535 HIS A4397 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.117697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.089379 restraints weight = 68195.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091874 restraints weight = 35031.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.093542 restraints weight = 23334.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094592 restraints weight = 18247.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095151 restraints weight = 15724.950| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.6227 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= 0.211 Angle : 0.721 12.212 32549 Z= 0.356 Chirality : 0.044 0.236 3651 Planarity : 0.005 0.066 4175 Dihedral : 6.054 123.638 3233 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 2.67 % Allowed : 23.93 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.16), residues: 2901 helix: 1.72 (0.13), residues: 1671 sheet: -1.01 (0.31), residues: 271 loop : 0.25 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2273 TYR 0.020 0.002 TYR A2748 PHE 0.024 0.002 PHE A1551 TRP 0.076 0.003 TRP A2584 HIS 0.011 0.001 HIS A4381 Details of bonding type rmsd covalent geometry : bond 0.00475 (24001) covalent geometry : angle 0.72071 (32549) hydrogen bonds : bond 0.04125 ( 1359) hydrogen bonds : angle 4.39645 ( 3954) *********************** 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 360 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 291 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7725 (ptp-110) cc_final: 0.7318 (ptp-170) REVERT: A 1837 GLU cc_start: 0.7912 (tp30) cc_final: 0.7088 (tp30) REVERT: A 1841 GLN cc_start: 0.8369 (mp10) cc_final: 0.7957 (mp10) REVERT: A 1967 MET cc_start: 0.8099 (mmm) cc_final: 0.7846 (mtp) REVERT: A 2012 MET cc_start: 0.8783 (tmm) cc_final: 0.8445 (tmm) REVERT: A 2294 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7100 (mp0) REVERT: A 2423 MET cc_start: 0.8859 (mtm) cc_final: 0.8598 (mtm) REVERT: A 2510 MET cc_start: 0.8528 (mpp) cc_final: 0.7993 (mtp) REVERT: A 2513 GLU cc_start: 0.7828 (tm-30) cc_final: 0.6778 (tm-30) REVERT: A 2537 TYR cc_start: 0.8140 (m-10) cc_final: 0.7690 (m-10) REVERT: A 2712 CYS cc_start: 0.7574 (m) cc_final: 0.7271 (m) REVERT: A 2851 ASP cc_start: 0.9185 (m-30) cc_final: 0.8673 (m-30) REVERT: A 2867 MET cc_start: 0.7437 (mtt) cc_final: 0.7184 (tpp) REVERT: A 2873 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.4670 (t80) REVERT: A 3007 ARG cc_start: 0.7864 (mtt-85) cc_final: 0.7513 (ptp-170) REVERT: A 3030 MET cc_start: 0.7434 (mmm) cc_final: 0.6559 (mmm) REVERT: A 3155 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8510 (t-90) REVERT: A 3193 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7743 (pt0) REVERT: A 3507 CYS cc_start: 0.8600 (m) cc_final: 0.8281 (m) REVERT: A 3521 ASP cc_start: 0.7907 (p0) cc_final: 0.7701 (p0) REVERT: A 3640 SER cc_start: 0.8405 (m) cc_final: 0.7948 (p) REVERT: A 3785 GLU cc_start: 0.4629 (OUTLIER) cc_final: 0.3963 (pt0) REVERT: A 3813 PHE cc_start: 0.8498 (m-10) cc_final: 0.8107 (m-10) REVERT: A 3819 LYS cc_start: 0.9176 (ptpt) cc_final: 0.8859 (ptpt) REVERT: A 3830 GLN cc_start: 0.9007 (tp40) cc_final: 0.8773 (tp40) REVERT: A 3906 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7729 (tp-100) REVERT: A 3994 GLN cc_start: 0.8515 (tt0) cc_final: 0.7903 (tm-30) REVERT: A 4128 MET cc_start: 0.8322 (pmm) cc_final: 0.7182 (ptp) REVERT: A 4157 MET cc_start: 0.9022 (mmm) cc_final: 0.8803 (mtp) REVERT: A 4338 ASP cc_start: 0.7732 (m-30) cc_final: 0.7500 (m-30) REVERT: A 4346 MET cc_start: 0.9017 (mmt) cc_final: 0.8483 (mmm) REVERT: A 4426 ASP cc_start: 0.8786 (t0) cc_final: 0.8402 (t0) REVERT: A 4430 ASP cc_start: 0.7363 (m-30) cc_final: 0.7148 (m-30) REVERT: A 4617 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8372 (p0) outliers start: 69 outliers final: 47 residues processed: 344 average time/residue: 0.1441 time to fit residues: 80.8631 Evaluate side-chains 319 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 2082 SER Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2487 GLU 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 2591 LEU 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 2666 ILE Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2873 TYR Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2962 LYS Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR 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 3835 ILE Chi-restraints excluded: chain A residue 3938 LEU Chi-restraints excluded: chain A residue 4027 LEU 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 4414 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 201 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 114 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1818 GLN A2005 GLN ** A2209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2439 HIS A2857 HIS A3155 HIS A3535 HIS A3584 ASN A3837 HIS A4137 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.118070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.090083 restraints weight = 68022.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092623 restraints weight = 34496.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094337 restraints weight = 22753.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095281 restraints weight = 17608.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.096015 restraints weight = 15228.194| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24001 Z= 0.156 Angle : 0.667 12.138 32549 Z= 0.324 Chirality : 0.042 0.233 3651 Planarity : 0.004 0.064 4175 Dihedral : 5.966 119.567 3233 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.72 % Rotamer: Outliers : 2.25 % Allowed : 24.62 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.16), residues: 2901 helix: 1.84 (0.13), residues: 1671 sheet: -0.98 (0.31), residues: 271 loop : 0.30 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A2610 TYR 0.024 0.001 TYR A2959 PHE 0.021 0.002 PHE A1551 TRP 0.074 0.002 TRP A2584 HIS 0.004 0.001 HIS A2791 Details of bonding type rmsd covalent geometry : bond 0.00356 (24001) covalent geometry : angle 0.66650 (32549) hydrogen bonds : bond 0.03828 ( 1359) hydrogen bonds : angle 4.30982 ( 3954) *********************** 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 352 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 ARG cc_start: 0.7693 (ptp-110) cc_final: 0.7273 (ptp-170) REVERT: A 1837 GLU cc_start: 0.7851 (tp30) cc_final: 0.7325 (tp30) REVERT: A 1841 GLN cc_start: 0.8382 (mp10) cc_final: 0.8109 (mp10) REVERT: A 1967 MET cc_start: 0.8171 (mmm) cc_final: 0.7968 (mtp) REVERT: A 2012 MET cc_start: 0.8783 (tmm) cc_final: 0.8473 (tmm) REVERT: A 2310 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 2447 MET cc_start: 0.6851 (mmt) cc_final: 0.6530 (tpp) REVERT: A 2510 MET cc_start: 0.8450 (mpp) cc_final: 0.7962 (mtp) REVERT: A 2513 GLU cc_start: 0.7875 (tm-30) cc_final: 0.6876 (tm-30) REVERT: A 2537 TYR cc_start: 0.8217 (m-10) cc_final: 0.7851 (m-10) REVERT: A 2607 SER cc_start: 0.8174 (t) cc_final: 0.7943 (p) REVERT: A 2665 GLU cc_start: 0.6822 (mp0) cc_final: 0.6398 (mp0) REVERT: A 2668 LEU cc_start: 0.8814 (mt) cc_final: 0.8605 (tp) REVERT: A 2688 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 2712 CYS cc_start: 0.7511 (m) cc_final: 0.7228 (m) REVERT: A 2779 MET cc_start: 0.8316 (tpp) cc_final: 0.8057 (ptp) REVERT: A 2851 ASP cc_start: 0.9171 (m-30) cc_final: 0.8677 (m-30) REVERT: A 2873 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.4501 (t80) REVERT: A 3030 MET cc_start: 0.7423 (mmm) cc_final: 0.6561 (mmm) REVERT: A 3126 MET cc_start: 0.5086 (pmm) cc_final: 0.4456 (pmm) REVERT: A 3193 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 3507 CYS cc_start: 0.8574 (m) cc_final: 0.8006 (t) REVERT: A 3521 ASP cc_start: 0.7953 (p0) cc_final: 0.7724 (p0) REVERT: A 3640 SER cc_start: 0.8409 (m) cc_final: 0.7933 (p) REVERT: A 3720 GLU cc_start: 0.7243 (tp30) cc_final: 0.6998 (tp30) REVERT: A 3785 GLU cc_start: 0.4504 (OUTLIER) cc_final: 0.3833 (pt0) REVERT: A 3813 PHE cc_start: 0.8457 (m-10) cc_final: 0.8077 (m-10) REVERT: A 3830 GLN cc_start: 0.8937 (tp40) cc_final: 0.8682 (tp40) REVERT: A 3906 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7721 (tp-100) REVERT: A 3994 GLN cc_start: 0.8431 (tt0) cc_final: 0.7708 (tm-30) REVERT: A 4128 MET cc_start: 0.8269 (pmm) cc_final: 0.7987 (ptp) REVERT: A 4346 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8688 (mmm) REVERT: A 4426 ASP cc_start: 0.8780 (t0) cc_final: 0.8377 (t0) REVERT: A 4430 ASP cc_start: 0.7481 (m-30) cc_final: 0.7212 (m-30) REVERT: A 4617 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8330 (p0) outliers start: 58 outliers final: 39 residues processed: 340 average time/residue: 0.1493 time to fit residues: 83.4910 Evaluate side-chains 312 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 2310 GLU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2446 ILE 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 2574 THR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2627 THR 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 2835 ASP Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2873 TYR Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2962 LYS Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3121 ILE 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 3835 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 4189 ILE Chi-restraints excluded: chain A residue 4246 LEU 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 4509 VAL Chi-restraints excluded: chain A residue 4516 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 18 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 287 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 251 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN A2187 GLN ** A2299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2857 HIS A3527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.119629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091687 restraints weight = 67733.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094269 restraints weight = 34243.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.095995 restraints weight = 22522.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096926 restraints weight = 17455.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097338 restraints weight = 15092.665| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24001 Z= 0.121 Angle : 0.660 12.830 32549 Z= 0.317 Chirality : 0.041 0.222 3651 Planarity : 0.004 0.044 4175 Dihedral : 5.832 114.485 3233 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.55 % Rotamer: Outliers : 1.82 % Allowed : 25.28 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.16), residues: 2901 helix: 1.91 (0.13), residues: 1671 sheet: -0.89 (0.33), residues: 257 loop : 0.31 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A2811 TYR 0.024 0.001 TYR A2193 PHE 0.023 0.001 PHE A3957 TRP 0.071 0.002 TRP A2584 HIS 0.004 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00270 (24001) covalent geometry : angle 0.65995 (32549) hydrogen bonds : bond 0.03633 ( 1359) hydrogen bonds : angle 4.21033 ( 3954) ********************** 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 354 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 307 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1837 GLU cc_start: 0.7853 (tp30) cc_final: 0.7293 (tp30) REVERT: A 1841 GLN cc_start: 0.8389 (mp10) cc_final: 0.8098 (mp10) REVERT: A 1967 MET cc_start: 0.8120 (mmm) cc_final: 0.7847 (mtp) REVERT: A 2012 MET cc_start: 0.8722 (tmm) cc_final: 0.8435 (tmm) REVERT: A 2310 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: A 2423 MET cc_start: 0.8843 (mtm) cc_final: 0.8580 (mtm) REVERT: A 2447 MET cc_start: 0.6872 (mmt) cc_final: 0.6568 (tpp) REVERT: A 2510 MET cc_start: 0.8492 (mpp) cc_final: 0.7930 (mtp) REVERT: A 2513 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7039 (tm-30) REVERT: A 2537 TYR cc_start: 0.8180 (m-10) cc_final: 0.7855 (m-10) REVERT: A 2665 GLU cc_start: 0.6666 (mp0) cc_final: 0.6261 (mp0) REVERT: A 2688 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 2712 CYS cc_start: 0.7547 (m) cc_final: 0.7225 (m) REVERT: A 2851 ASP cc_start: 0.8820 (m-30) cc_final: 0.8532 (m-30) REVERT: A 2867 MET cc_start: 0.8343 (tpp) cc_final: 0.8136 (tmm) REVERT: A 2873 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.4569 (t80) REVERT: A 2982 ARG cc_start: 0.8619 (mmt-90) cc_final: 0.8118 (ttm110) REVERT: A 3030 MET cc_start: 0.7430 (mmm) cc_final: 0.6640 (mmm) REVERT: A 3113 MET cc_start: 0.8211 (mmp) cc_final: 0.7924 (mmt) REVERT: A 3126 MET cc_start: 0.5061 (pmm) cc_final: 0.4445 (pmm) REVERT: A 3507 CYS cc_start: 0.8451 (m) cc_final: 0.7850 (t) REVERT: A 3640 SER cc_start: 0.8334 (m) cc_final: 0.7899 (p) REVERT: A 3785 GLU cc_start: 0.4627 (OUTLIER) cc_final: 0.3955 (pt0) REVERT: A 3813 PHE cc_start: 0.8416 (m-10) cc_final: 0.8065 (m-10) REVERT: A 3830 GLN cc_start: 0.8919 (tp40) cc_final: 0.8701 (tp40) REVERT: A 3906 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7717 (tp-100) REVERT: A 3994 GLN cc_start: 0.8412 (tt0) cc_final: 0.7696 (tm-30) REVERT: A 4043 MET cc_start: 0.9153 (mmm) cc_final: 0.8890 (mmm) REVERT: A 4128 MET cc_start: 0.8216 (pmm) cc_final: 0.7110 (ptp) REVERT: A 4262 GLN cc_start: 0.8681 (mm-40) cc_final: 0.7935 (tp-100) REVERT: A 4346 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8597 (mmm) REVERT: A 4426 ASP cc_start: 0.8775 (t0) cc_final: 0.8372 (t0) REVERT: A 4430 ASP cc_start: 0.7326 (m-30) cc_final: 0.7126 (m-30) REVERT: A 4617 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8414 (p0) outliers start: 47 outliers final: 33 residues processed: 343 average time/residue: 0.1601 time to fit residues: 89.0750 Evaluate side-chains 322 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 284 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 2310 GLU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2448 ASP 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 2627 THR 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 2799 MET Chi-restraints excluded: chain A residue 2857 HIS Chi-restraints excluded: chain A residue 2873 TYR Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2962 LYS Chi-restraints excluded: chain A residue 3121 ILE 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 3938 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4246 LEU Chi-restraints excluded: chain A residue 4346 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 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 258 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 273 optimal weight: 0.0980 chunk 142 optimal weight: 0.9980 chunk 230 optimal weight: 0.2980 chunk 161 optimal weight: 6.9990 chunk 158 optimal weight: 0.0470 chunk 246 optimal weight: 0.6980 chunk 254 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2134 GLN ** A2212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2857 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.120248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.092778 restraints weight = 67712.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.095327 restraints weight = 33854.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.097019 restraints weight = 22141.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098022 restraints weight = 17079.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.098577 restraints weight = 14695.187| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24001 Z= 0.119 Angle : 0.665 12.520 32549 Z= 0.318 Chirality : 0.041 0.214 3651 Planarity : 0.004 0.047 4175 Dihedral : 5.728 111.716 3233 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.62 % Rotamer: Outliers : 1.70 % Allowed : 25.78 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.16), residues: 2901 helix: 1.93 (0.13), residues: 1670 sheet: -0.82 (0.32), residues: 255 loop : 0.32 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A2811 TYR 0.027 0.001 TYR A2193 PHE 0.030 0.002 PHE A2992 TRP 0.070 0.002 TRP A2584 HIS 0.021 0.001 HIS A2857 Details of bonding type rmsd covalent geometry : bond 0.00265 (24001) covalent geometry : angle 0.66543 (32549) hydrogen bonds : bond 0.03551 ( 1359) hydrogen bonds : angle 4.19770 ( 3954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5210.13 seconds wall clock time: 90 minutes 12.76 seconds (5412.76 seconds total)