Starting phenix.real_space_refine on Tue Oct 27 17:33:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27py_81335/10_2026/27py_81335.cif Found real_map, /net/cci-nas-00/data/ceres_data/27py_81335/10_2026/27py_81335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/27py_81335/10_2026/27py_81335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27py_81335/10_2026/27py_81335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/27py_81335/10_2026/27py_81335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27py_81335/10_2026/27py_81335.map" } resolution = 2.61 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= 0.001 sd= 0.053 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 98 5.16 5 C 15615 2.51 5 N 4174 2.21 5 O 4621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24518 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3034, 24405 Classifications: {'peptide': 3034} Link IDs: {'PCIS': 4, 'PTRANS': 122, 'TRANS': 2907} Chain breaks: 4 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: 4.80, per 1000 atoms: 0.20 Number of scatterers: 24518 At special positions: 0 Unit cell: (118.728, 154.521, 174.6, 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 98 16.00 P 9 15.00 Mg 1 11.99 O 4621 8.00 N 4174 7.00 C 15615 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: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5782 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 21 sheets defined 64.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 1400 through 1417 removed outlier: 3.783A pdb=" N LEU A1404 " --> pdb=" O VAL A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1441 removed outlier: 3.565A pdb=" N ARG A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A1432 " --> pdb=" O ARG A1428 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A1440 " --> pdb=" O GLN A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1464 removed outlier: 4.624A pdb=" N GLN A1455 " --> pdb=" O PHE A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1473 Processing helix chain 'A' and resid 1477 through 1488 removed outlier: 3.855A pdb=" N TRP A1481 " --> pdb=" O LYS A1477 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1483 " --> pdb=" O ARG A1479 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A1485 " --> pdb=" O TRP A1481 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LYS A1486 " --> pdb=" O LYS A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1505 removed outlier: 3.522A pdb=" N SER A1505 " --> pdb=" O SER A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1518 removed outlier: 5.105A pdb=" N ILE A1513 " --> pdb=" O ARG A1509 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLU A1516 " --> pdb=" O ASN A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1541 removed outlier: 3.928A pdb=" N GLN A1522 " --> pdb=" O ILE A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1578 removed outlier: 3.546A pdb=" N MET A1577 " --> pdb=" O SER A1573 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A1578 " --> pdb=" O ALA A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1620 removed outlier: 3.514A pdb=" N ALA A1588 " --> pdb=" O PHE A1584 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A1607 " --> pdb=" O ASP A1603 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A1617 " --> pdb=" O VAL A1613 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A1618 " --> pdb=" O TYR A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1629 Processing helix chain 'A' and resid 1629 through 1653 Processing helix chain 'A' and resid 1655 through 1661 Processing helix chain 'A' and resid 1664 through 1694 Processing helix chain 'A' and resid 1695 through 1700 Processing helix chain 'A' and resid 1701 through 1711 Processing helix chain 'A' and resid 1714 through 1719 Processing helix chain 'A' and resid 1721 through 1726 Processing helix chain 'A' and resid 1765 through 1793 Processing helix chain 'A' and resid 1799 through 1810 removed outlier: 3.694A pdb=" N TYR A1810 " --> pdb=" O TRP A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1811 through 1832 Processing helix chain 'A' and resid 1837 through 1864 removed outlier: 3.799A pdb=" N LEU A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1894 Processing helix chain 'A' and resid 1903 through 1908 Processing helix chain 'A' and resid 1920 through 1923 Processing helix chain 'A' and resid 1950 through 1966 Processing helix chain 'A' and resid 1979 through 1991 Processing helix chain 'A' and resid 2005 through 2020 Processing helix chain 'A' and resid 2027 through 2031 Processing helix chain 'A' and resid 2032 through 2052 removed outlier: 3.547A pdb=" N GLN A2042 " --> pdb=" O ALA A2038 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2084 removed outlier: 4.145A pdb=" N GLY A2083 " --> pdb=" O GLY A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2091 through 2093 No H-bonds generated for 'chain 'A' and resid 2091 through 2093' Processing helix chain 'A' and resid 2104 through 2112 Processing helix chain 'A' and resid 2120 through 2139 Proline residue: A2130 - end of helix Processing helix chain 'A' and resid 2148 through 2166 Processing helix chain 'A' and resid 2176 through 2203 Processing helix chain 'A' and resid 2204 through 2207 Processing helix chain 'A' and resid 2208 through 2209 No H-bonds generated for 'chain 'A' and resid 2208 through 2209' Processing helix chain 'A' and resid 2210 through 2223 removed outlier: 4.134A pdb=" N LEU A2214 " --> pdb=" O ASP A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2233 through 2247 Processing helix chain 'A' and resid 2252 through 2269 Processing helix chain 'A' and resid 2281 through 2298 Processing helix chain 'A' and resid 2312 through 2317 Processing helix chain 'A' and resid 2330 through 2341 Processing helix chain 'A' and resid 2360 through 2365 Processing helix chain 'A' and resid 2367 through 2372 Processing helix chain 'A' and resid 2404 through 2410 removed outlier: 3.500A pdb=" N ARG A2410 " --> pdb=" O ALA A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 2422 through 2435 Processing helix chain 'A' and resid 2440 through 2456 Processing helix chain 'A' and resid 2489 through 2503 Processing helix chain 'A' and resid 2504 through 2507 removed outlier: 3.669A pdb=" N GLU A2507 " --> pdb=" O GLN A2504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2504 through 2507' Processing helix chain 'A' and resid 2510 through 2521 removed outlier: 3.501A pdb=" N GLN A2521 " --> pdb=" O GLU A2517 " (cutoff:3.500A) Processing helix chain 'A' and resid 2529 through 2555 Processing helix chain 'A' and resid 2561 through 2582 Processing helix chain 'A' and resid 2586 through 2601 Processing helix chain 'A' and resid 2611 through 2613 No H-bonds generated for 'chain 'A' and resid 2611 through 2613' Processing helix chain 'A' and resid 2628 through 2631 Processing helix chain 'A' and resid 2650 through 2666 removed outlier: 3.682A pdb=" N ALA A2662 " --> pdb=" O ASP A2658 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP A2663 " --> pdb=" O VAL A2659 " (cutoff:3.500A) Processing helix chain 'A' and resid 2679 through 2690 Processing helix chain 'A' and resid 2706 through 2717 removed outlier: 3.712A pdb=" N LEU A2710 " --> pdb=" O THR A2706 " (cutoff:3.500A) Processing helix chain 'A' and resid 2757 through 2769 Processing helix chain 'A' and resid 2804 through 2809 Processing helix chain 'A' and resid 2820 through 2836 removed outlier: 3.584A pdb=" N ALA A2834 " --> pdb=" O THR A2830 " (cutoff:3.500A) Processing helix chain 'A' and resid 2837 through 2844 Proline residue: A2840 - end of helix removed outlier: 4.996A pdb=" N SER A2844 " --> pdb=" O ASN A2841 " (cutoff:3.500A) Processing helix chain 'A' and resid 2845 through 2864 Processing helix chain 'A' and resid 2875 through 2893 removed outlier: 3.947A pdb=" N LEU A2879 " --> pdb=" O SER A2875 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A2892 " --> pdb=" O GLU A2888 " (cutoff:3.500A) Processing helix chain 'A' and resid 2897 through 2914 Processing helix chain 'A' and resid 2919 through 2938 Processing helix chain 'A' and resid 2942 through 2947 removed outlier: 3.574A pdb=" N LYS A2947 " --> pdb=" O ASP A2944 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2983 removed outlier: 3.696A pdb=" N VAL A2978 " --> pdb=" O ALA A2974 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A2981 " --> pdb=" O LYS A2977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3006 Processing helix chain 'A' and resid 3021 through 3033 Processing helix chain 'A' and resid 3047 through 3064 Processing helix chain 'A' and resid 3076 through 3078 No H-bonds generated for 'chain 'A' and resid 3076 through 3078' Processing helix chain 'A' and resid 3080 through 3094 removed outlier: 3.728A pdb=" N LEU A3084 " --> pdb=" O GLU A3080 " (cutoff:3.500A) Processing helix chain 'A' and resid 3102 through 3114 removed outlier: 3.882A pdb=" N GLU A3114 " --> pdb=" O HIS A3110 " (cutoff:3.500A) Processing helix chain 'A' and resid 3125 through 3139 removed outlier: 4.470A pdb=" N VAL A3137 " --> pdb=" O PHE A3133 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3161 removed outlier: 4.211A pdb=" N SER A3158 " --> pdb=" O PHE A3154 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA A3159 " --> pdb=" O HIS A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3161 through 3167 removed outlier: 4.394A pdb=" N PHE A3165 " --> pdb=" O SER A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3177 through 3189 Processing helix chain 'A' and resid 3202 through 3212 removed outlier: 3.521A pdb=" N GLU A3208 " --> pdb=" O VAL A3204 " (cutoff:3.500A) Processing helix chain 'A' and resid 3222 through 3249 Processing helix chain 'A' and resid 3256 through 3306 removed outlier: 3.766A pdb=" N VAL A3304 " --> pdb=" O LYS A3300 " (cutoff:3.500A) Processing helix chain 'A' and resid 3554 through 3587 Processing helix chain 'A' and resid 3587 through 3602 Processing helix chain 'A' and resid 3603 through 3605 No H-bonds generated for 'chain 'A' and resid 3603 through 3605' Processing helix chain 'A' and resid 3606 through 3625 Processing helix chain 'A' and resid 3633 through 3638 Processing helix chain 'A' and resid 3640 through 3650 Processing helix chain 'A' and resid 3655 through 3668 Processing helix chain 'A' and resid 3679 through 3689 Processing helix chain 'A' and resid 3703 through 3715 Processing helix chain 'A' and resid 3727 through 3729 No H-bonds generated for 'chain 'A' and resid 3727 through 3729' Processing helix chain 'A' and resid 3730 through 3735 Processing helix chain 'A' and resid 3774 through 3781 Processing helix chain 'A' and resid 3789 through 3806 Processing helix chain 'A' and resid 3806 through 3831 removed outlier: 3.621A pdb=" N HIS A3810 " --> pdb=" O ARG A3806 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A3825 " --> pdb=" O GLY A3821 " (cutoff:3.500A) Processing helix chain 'A' and resid 3833 through 3841 Processing helix chain 'A' and resid 3842 through 3847 removed outlier: 5.260A pdb=" N ILE A3845 " --> pdb=" O SER A3842 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A3846 " --> pdb=" O GLY A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3848 through 3903 removed outlier: 4.065A pdb=" N ILE A3852 " --> pdb=" O ASP A3848 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A3884 " --> pdb=" O SER A3880 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A3886 " --> pdb=" O VAL A3882 " (cutoff:3.500A) Proline residue: A3888 - end of helix Processing helix chain 'A' and resid 3904 through 3906 No H-bonds generated for 'chain 'A' and resid 3904 through 3906' Processing helix chain 'A' and resid 3912 through 3926 Processing helix chain 'A' and resid 3927 through 3931 Processing helix chain 'A' and resid 3935 through 3956 removed outlier: 3.676A pdb=" N TYR A3942 " --> pdb=" O GLU A3938 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A3945 " --> pdb=" O VAL A3941 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A3947 " --> pdb=" O LEU A3943 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE A3948 " --> pdb=" O SER A3944 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A3949 " --> pdb=" O LYS A3945 " (cutoff:3.500A) Processing helix chain 'A' and resid 3960 through 3977 removed outlier: 4.403A pdb=" N LEU A3965 " --> pdb=" O ASN A3961 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A3966 " --> pdb=" O ASP A3962 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A3977 " --> pdb=" O ILE A3973 " (cutoff:3.500A) Processing helix chain 'A' and resid 3984 through 3994 Processing helix chain 'A' and resid 4005 through 4009 removed outlier: 3.582A pdb=" N ASP A4009 " --> pdb=" O PRO A4006 " (cutoff:3.500A) Processing helix chain 'A' and resid 4013 through 4027 Processing helix chain 'A' and resid 4028 through 4031 Processing helix chain 'A' and resid 4032 through 4040 Processing helix chain 'A' and resid 4040 through 4049 removed outlier: 5.133A pdb=" N GLN A4046 " --> pdb=" O SER A4042 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A4047 " --> pdb=" O ASP A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4069 Processing helix chain 'A' and resid 4074 through 4089 removed outlier: 3.536A pdb=" N SER A4078 " --> pdb=" O SER A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4090 through 4092 No H-bonds generated for 'chain 'A' and resid 4090 through 4092' Processing helix chain 'A' and resid 4093 through 4104 Processing helix chain 'A' and resid 4117 through 4125 Processing helix chain 'A' and resid 4142 through 4153 removed outlier: 3.648A pdb=" N VAL A4146 " --> pdb=" O ALA A4142 " (cutoff:3.500A) Processing helix chain 'A' and resid 4166 through 4182 removed outlier: 3.681A pdb=" N LEU A4170 " --> pdb=" O GLU A4166 " (cutoff:3.500A) Processing helix chain 'A' and resid 4189 through 4192 removed outlier: 3.632A pdb=" N LEU A4192 " --> pdb=" O ASN A4189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4189 through 4192' Processing helix chain 'A' and resid 4193 through 4206 removed outlier: 4.268A pdb=" N VAL A4198 " --> pdb=" O PRO A4194 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN A4199 " --> pdb=" O GLN A4195 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A4206 " --> pdb=" O LYS A4202 " (cutoff:3.500A) Processing helix chain 'A' and resid 4226 through 4232 removed outlier: 3.554A pdb=" N MET A4232 " --> pdb=" O ASN A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4243 through 4254 removed outlier: 3.843A pdb=" N GLY A4254 " --> pdb=" O HIS A4250 " (cutoff:3.500A) Processing helix chain 'A' and resid 4256 through 4261 Processing helix chain 'A' and resid 4265 through 4284 removed outlier: 4.197A pdb=" N ARG A4269 " --> pdb=" O ALA A4265 " (cutoff:3.500A) Processing helix chain 'A' and resid 4285 through 4288 removed outlier: 4.017A pdb=" N ILE A4288 " --> pdb=" O LEU A4285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4285 through 4288' Processing helix chain 'A' and resid 4299 through 4318 Processing helix chain 'A' and resid 4330 through 4341 removed outlier: 3.604A pdb=" N VAL A4334 " --> pdb=" O PRO A4330 " (cutoff:3.500A) Processing helix chain 'A' and resid 4349 through 4364 Processing helix chain 'A' and resid 4365 through 4370 Processing helix chain 'A' and resid 4389 through 4398 Processing helix chain 'A' and resid 4404 through 4409 removed outlier: 3.513A pdb=" N GLY A4409 " --> pdb=" O ILE A4406 " (cutoff:3.500A) Processing helix chain 'A' and resid 4412 through 4442 removed outlier: 3.902A pdb=" N SER A4416 " --> pdb=" O GLU A4412 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A4436 " --> pdb=" O LYS A4432 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU A4437 " --> pdb=" O MET A4433 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A4440 " --> pdb=" O SER A4436 " (cutoff:3.500A) Processing helix chain 'A' and resid 4460 through 4477 removed outlier: 3.508A pdb=" N LYS A4475 " --> pdb=" O THR A4471 " (cutoff:3.500A) Processing helix chain 'A' and resid 4489 through 4492 Processing helix chain 'A' and resid 4493 through 4525 removed outlier: 4.154A pdb=" N SER A4525 " --> pdb=" O LEU A4521 " (cutoff:3.500A) Processing helix chain 'A' and resid 4531 through 4544 removed outlier: 3.789A pdb=" N THR A4539 " --> pdb=" O ARG A4535 " (cutoff:3.500A) Processing helix chain 'A' and resid 4547 through 4551 removed outlier: 3.650A pdb=" N TRP A4550 " --> pdb=" O PRO A4547 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4580 Processing helix chain 'A' and resid 4592 through 4594 No H-bonds generated for 'chain 'A' and resid 4592 through 4594' Processing helix chain 'A' and resid 4596 through 4613 Processing helix chain 'A' and resid 4615 through 4617 No H-bonds generated for 'chain 'A' and resid 4615 through 4617' Processing helix chain 'A' and resid 4676 through 4685 removed outlier: 4.531A pdb=" N ASN A4681 " --> pdb=" O ILE A4678 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A4683 " --> pdb=" O ASN A4680 " (cutoff:3.500A) Processing helix chain 'A' and resid 4712 through 4720 removed outlier: 3.850A pdb=" N SER A4720 " --> pdb=" O TRP A4716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1544 through 1548 removed outlier: 4.310A pdb=" N ASP A1544 " --> pdb=" O ARG A1556 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A1552 " --> pdb=" O TYR A1548 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1731 through 1734 removed outlier: 7.147A pdb=" N GLY A1743 " --> pdb=" O LYS A1756 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N LYS A1756 " --> pdb=" O GLY A1743 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N SER A1745 " --> pdb=" O PHE A1754 " (cutoff:3.500A) removed outlier: 10.890A pdb=" N PHE A1754 " --> pdb=" O SER A1745 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1911 through 1914 Processing sheet with id=AA4, first strand: chain 'A' and resid 1969 through 1973 Processing sheet with id=AA5, first strand: chain 'A' and resid 1995 through 1999 Processing sheet with id=AA6, first strand: chain 'A' and resid 2056 through 2057 Processing sheet with id=AA7, first strand: chain 'A' and resid 2301 through 2306 removed outlier: 6.486A pdb=" N HIS A2351 " --> pdb=" O ARG A2392 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N MET A2394 " --> pdb=" O HIS A2351 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE A2353 " --> pdb=" O MET A2394 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLU A2396 " --> pdb=" O ILE A2353 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE A2355 " --> pdb=" O GLU A2396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2318 through 2320 Processing sheet with id=AA9, first strand: chain 'A' and resid 2376 through 2377 Processing sheet with id=AB1, first strand: chain 'A' and resid 2615 through 2618 removed outlier: 3.592A pdb=" N ASN A2623 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2694 through 2699 removed outlier: 6.666A pdb=" N ILE A2671 " --> pdb=" O LEU A2814 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2718 through 2722 removed outlier: 4.361A pdb=" N THR A2728 " --> pdb=" O TRP A2780 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2951 through 2953 removed outlier: 4.340A pdb=" N LEU A2951 " --> pdb=" O VAL A2963 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3036 through 3038 removed outlier: 6.423A pdb=" N ALA A3012 " --> pdb=" O PHE A3145 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET A3147 " --> pdb=" O ALA A3012 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A3014 " --> pdb=" O MET A3147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3695 through 3698 Processing sheet with id=AB7, first strand: chain 'A' and resid 3738 through 3739 Processing sheet with id=AB8, first strand: chain 'A' and resid 4159 through 4160 removed outlier: 6.161A pdb=" N VAL A4185 " --> pdb=" O PHE A4216 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR A4218 " --> pdb=" O VAL A4185 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A4187 " --> pdb=" O THR A4218 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N GLU A4220 " --> pdb=" O LEU A4187 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A4133 " --> pdb=" O PHE A4236 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TYR A4238 " --> pdb=" O LEU A4133 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N CYS A4135 " --> pdb=" O TYR A4238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4374 through 4376 Processing sheet with id=AC1, first strand: chain 'A' and resid 4588 through 4590 removed outlier: 6.580A pdb=" N THR A4668 " --> pdb=" O SER A4624 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4661 through 4663 Processing sheet with id=AC3, first strand: chain 'A' and resid 4648 through 4650 1462 hydrogen bonds defined for protein. 4254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.71 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7999 1.34 - 1.46: 4057 1.46 - 1.57: 12811 1.57 - 1.69: 14 1.69 - 1.81: 165 Bond restraints: 25046 Sorted by residual: bond pdb=" C4 ADP A5001 " pdb=" C5 ADP A5001 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C4 ADP A5005 " pdb=" C5 ADP A5005 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C4 ADP A5004 " pdb=" C5 ADP A5004 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C5 ADP A5001 " pdb=" C6 ADP A5001 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C5 ADP A5005 " pdb=" C6 ADP A5005 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 25041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 33864 3.80 - 7.60: 71 7.60 - 11.40: 17 11.40 - 15.20: 0 15.20 - 19.01: 3 Bond angle restraints: 33955 Sorted by residual: angle pdb=" PA ADP A5004 " pdb=" O3A ADP A5004 " pdb=" PB ADP A5004 " ideal model delta sigma weight residual 120.50 139.51 -19.01 3.00e+00 1.11e-01 4.01e+01 angle pdb=" PB ATP A5002 " pdb=" O3B ATP A5002 " pdb=" PG ATP A5002 " ideal model delta sigma weight residual 139.87 133.70 6.17 1.00e+00 1.00e+00 3.81e+01 angle pdb=" PA ADP A5001 " pdb=" O3A ADP A5001 " pdb=" PB ADP A5001 " ideal model delta sigma weight residual 120.50 138.82 -18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" PA ADP A5005 " pdb=" O3A ADP A5005 " pdb=" PB ADP A5005 " ideal model delta sigma weight residual 120.50 136.87 -16.37 3.00e+00 1.11e-01 2.98e+01 angle pdb=" C ALA A1930 " pdb=" N ASN A1931 " pdb=" CA ASN A1931 " ideal model delta sigma weight residual 125.66 133.18 -7.52 1.85e+00 2.92e-01 1.65e+01 ... (remaining 33950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 14920 35.71 - 71.41: 226 71.41 - 107.12: 16 107.12 - 142.82: 2 142.82 - 178.53: 2 Dihedral angle restraints: 15166 sinusoidal: 6280 harmonic: 8886 Sorted by residual: dihedral pdb=" O2A ADP A5004 " pdb=" O3A ADP A5004 " pdb=" PA ADP A5004 " pdb=" PB ADP A5004 " ideal model delta sinusoidal sigma weight residual -60.00 118.53 -178.53 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP A5001 " pdb=" O3A ADP A5001 " pdb=" PB ADP A5001 " pdb=" PA ADP A5001 " ideal model delta sinusoidal sigma weight residual -60.00 99.93 -159.93 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O1B ADP A5004 " pdb=" O3A ADP A5004 " pdb=" PB ADP A5004 " pdb=" PA ADP A5004 " ideal model delta sinusoidal sigma weight residual -60.00 -178.34 118.34 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 15163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2592 0.034 - 0.067: 896 0.067 - 0.101: 241 0.101 - 0.134: 82 0.134 - 0.168: 6 Chirality restraints: 3817 Sorted by residual: chirality pdb=" C3' ADP A5001 " pdb=" C2' ADP A5001 " pdb=" C4' ADP A5001 " pdb=" O3' ADP A5001 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ILE A4288 " pdb=" N ILE A4288 " pdb=" C ILE A4288 " pdb=" CB ILE A4288 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CA ILE A4058 " pdb=" N ILE A4058 " pdb=" C ILE A4058 " pdb=" CB ILE A4058 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 3814 not shown) Planarity restraints: 4327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1605 " 0.017 2.00e-02 2.50e+03 1.76e-02 7.74e+00 pdb=" CG TRP A1605 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A1605 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A1605 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1605 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A1605 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1605 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1605 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1605 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1605 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A2852 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C ALA A2852 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A2852 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A2853 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A2851 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ASP A2851 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP A2851 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A2852 " 0.012 2.00e-02 2.50e+03 ... (remaining 4324 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 163 2.59 - 3.17: 21000 3.17 - 3.75: 40109 3.75 - 4.32: 56097 4.32 - 4.90: 91368 Nonbonded interactions: 208737 Sorted by model distance: nonbonded pdb=" OG1 THR A2283 " pdb="MG MG A5003 " model vdw 2.017 2.170 nonbonded pdb=" O1G ATP A5002 " pdb="MG MG A5003 " model vdw 2.048 2.170 nonbonded pdb=" OG SER A4615 " pdb=" OE1 GLU A4617 " model vdw 2.166 3.040 nonbonded pdb=" OE2 GLU A3724 " pdb=" OG1 THR A3766 " model vdw 2.184 3.040 nonbonded pdb=" O ARG A4535 " pdb=" OG1 THR A4538 " model vdw 2.223 3.040 ... (remaining 208732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.470 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: 0.010 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 : 0.003 0.112 25046 Z= 0.154 Angle : 0.584 19.006 33955 Z= 0.287 Chirality : 0.038 0.168 3817 Planarity : 0.004 0.046 4327 Dihedral : 13.823 178.526 9384 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 1.67 (0.16), residues: 3024 helix: 1.55 (0.12), residues: 1760 sheet: -0.46 (0.32), residues: 257 loop : 0.99 (0.21), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2449 TYR 0.019 0.001 TYR A3897 PHE 0.020 0.001 PHE A3898 TRP 0.046 0.001 TRP A1605 HIS 0.004 0.001 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (25046) covalent geometry : angle 0.58413 / 0.29 (33955) hydrogen bonds : bond 0.12556 / 8.50 ( 1462) hydrogen bonds : angle 5.64409 / 4.15 ( 4254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.931 Fit side-chains REVERT: A 1547 ASN cc_start: 0.7518 (t0) cc_final: 0.7085 (t0) REVERT: A 1624 ASP cc_start: 0.7809 (m-30) cc_final: 0.7479 (m-30) REVERT: A 1670 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6951 (mt-10) REVERT: A 1723 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7612 (mmp-170) REVERT: A 2030 ARG cc_start: 0.8173 (mtt90) cc_final: 0.7895 (mtm180) REVERT: A 2078 ASN cc_start: 0.8153 (m110) cc_final: 0.7938 (m110) REVERT: A 2136 GLN cc_start: 0.8572 (tt0) cc_final: 0.8314 (tt0) REVERT: A 2253 GLN cc_start: 0.8547 (tt0) cc_final: 0.8327 (tt0) REVERT: A 2338 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7277 (ttp80) REVERT: A 2487 MET cc_start: 0.5206 (mmt) cc_final: 0.4765 (tpt) REVERT: A 2541 MET cc_start: 0.8753 (tpt) cc_final: 0.8456 (tpt) REVERT: A 2563 GLU cc_start: 0.7101 (tp30) cc_final: 0.6718 (tp30) REVERT: A 2591 GLU cc_start: 0.8062 (tt0) cc_final: 0.7831 (mm-30) REVERT: A 2628 LYS cc_start: 0.7827 (mttt) cc_final: 0.7588 (mtmt) REVERT: A 2721 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7615 (ttmm) REVERT: A 2845 PHE cc_start: 0.7839 (m-80) cc_final: 0.7636 (m-80) REVERT: A 2943 LEU cc_start: 0.8335 (mm) cc_final: 0.8033 (mp) REVERT: A 2961 GLN cc_start: 0.8223 (pt0) cc_final: 0.7447 (pm20) REVERT: A 2970 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7296 (mt-10) REVERT: A 2975 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7640 (mmm-85) REVERT: A 2981 GLU cc_start: 0.7320 (pt0) cc_final: 0.7078 (pt0) REVERT: A 3027 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7310 (mtp85) REVERT: A 3109 MET cc_start: 0.6091 (mmp) cc_final: 0.5628 (mpp) REVERT: A 3190 ARG cc_start: 0.6818 (ttm110) cc_final: 0.6601 (ptp90) REVERT: A 3273 GLU cc_start: 0.7945 (tt0) cc_final: 0.7677 (tt0) REVERT: A 3277 GLN cc_start: 0.7003 (mt0) cc_final: 0.6589 (mt0) REVERT: A 3656 GLU cc_start: 0.7862 (tp30) cc_final: 0.7448 (tp30) REVERT: A 3686 MET cc_start: 0.8268 (mmm) cc_final: 0.8041 (mmm) REVERT: A 3697 THR cc_start: 0.7600 (t) cc_final: 0.7334 (p) REVERT: A 3735 ASN cc_start: 0.6960 (m-40) cc_final: 0.6571 (m110) REVERT: A 3905 GLN cc_start: 0.7847 (mm110) cc_final: 0.6872 (pp30) REVERT: A 3929 ASN cc_start: 0.7768 (t0) cc_final: 0.7525 (m-40) REVERT: A 4322 SER cc_start: 0.8703 (m) cc_final: 0.8368 (p) REVERT: A 4372 ASP cc_start: 0.7724 (m-30) cc_final: 0.7440 (m-30) REVERT: A 4501 ARG cc_start: 0.7448 (ttt180) cc_final: 0.6727 (ttm170) REVERT: A 4548 LYS cc_start: 0.7706 (mptt) cc_final: 0.7469 (mptp) REVERT: A 4675 ASP cc_start: 0.7268 (m-30) cc_final: 0.7039 (m-30) outliers start: 0 outliers final: 1 residues processed: 363 average time/residue: 0.6587 time to fit residues: 274.3814 Evaluate side-chains 278 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3585 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.0270 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1719 GLN A1791 HIS A1846 GLN A1971 ASN A2235 GLN A2608 ASN A2734 GLN A2826 GLN A3669 ASN A3687 ASN A3926 ASN A4240 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.197989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139250 restraints weight = 24195.616| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.90 r_work: 0.3346 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25046 Z= 0.112 Angle : 0.514 8.928 33955 Z= 0.261 Chirality : 0.039 0.162 3817 Planarity : 0.004 0.064 4327 Dihedral : 6.987 149.287 3321 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.95 % Allowed : 6.11 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 1.96 (0.16), residues: 3024 helix: 1.86 (0.12), residues: 1785 sheet: -0.30 (0.32), residues: 254 loop : 0.91 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2392 TYR 0.018 0.001 TYR A3897 PHE 0.018 0.001 PHE A3898 TRP 0.027 0.001 TRP A1605 HIS 0.005 0.001 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (25046) covalent geometry : angle 0.51406 / 0.26 (33955) hydrogen bonds : bond 0.04246 / 2.82 ( 1462) hydrogen bonds : angle 4.42696 / 3.29 ( 4254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 1547 ASN cc_start: 0.7594 (t0) cc_final: 0.7156 (t0) REVERT: A 1624 ASP cc_start: 0.7636 (m-30) cc_final: 0.7332 (m-30) REVERT: A 1670 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6969 (mt-10) REVERT: A 1723 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7347 (mmm160) REVERT: A 1776 GLU cc_start: 0.8848 (tp30) cc_final: 0.8487 (tp30) REVERT: A 2030 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7529 (mtm180) REVERT: A 2136 GLN cc_start: 0.8303 (tt0) cc_final: 0.7965 (tt0) REVERT: A 2338 ARG cc_start: 0.7541 (ttm110) cc_final: 0.6991 (ttp80) REVERT: A 2358 ASP cc_start: 0.8226 (m-30) cc_final: 0.7887 (m-30) REVERT: A 2440 ASP cc_start: 0.7307 (t0) cc_final: 0.7011 (t0) REVERT: A 2487 MET cc_start: 0.5177 (mmt) cc_final: 0.4919 (tpt) REVERT: A 2541 MET cc_start: 0.8723 (tpt) cc_final: 0.8415 (tpt) REVERT: A 2563 GLU cc_start: 0.7022 (tp30) cc_final: 0.6686 (tp30) REVERT: A 2628 LYS cc_start: 0.7560 (mttt) cc_final: 0.7351 (mtmt) REVERT: A 2721 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7519 (ttmm) REVERT: A 2861 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: A 2921 GLU cc_start: 0.7042 (pm20) cc_final: 0.6749 (pp20) REVERT: A 2943 LEU cc_start: 0.8395 (mm) cc_final: 0.8110 (mp) REVERT: A 2948 ARG cc_start: 0.8985 (mmt-90) cc_final: 0.8770 (mpt-90) REVERT: A 2961 GLN cc_start: 0.8024 (pt0) cc_final: 0.7343 (pm20) REVERT: A 2970 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7144 (mt-10) REVERT: A 2975 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7583 (mmm-85) REVERT: A 3027 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7098 (mtp85) REVERT: A 3109 MET cc_start: 0.6212 (mmp) cc_final: 0.5692 (mpp) REVERT: A 3281 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6200 (mt-10) REVERT: A 3583 THR cc_start: 0.6871 (OUTLIER) cc_final: 0.6508 (p) REVERT: A 3656 GLU cc_start: 0.7483 (tp30) cc_final: 0.7110 (tp30) REVERT: A 3800 GLU cc_start: 0.7978 (tp30) cc_final: 0.7252 (tt0) REVERT: A 3905 GLN cc_start: 0.7637 (mm110) cc_final: 0.6805 (pp30) REVERT: A 4039 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.7011 (mt0) REVERT: A 4372 ASP cc_start: 0.7622 (m-30) cc_final: 0.7363 (m-30) REVERT: A 4431 GLN cc_start: 0.7746 (tt0) cc_final: 0.7273 (tp-100) REVERT: A 4501 ARG cc_start: 0.7190 (ttt180) cc_final: 0.6553 (ttm170) REVERT: A 4548 LYS cc_start: 0.7321 (mptt) cc_final: 0.7109 (mptp) REVERT: A 4645 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: A 4675 ASP cc_start: 0.7616 (m-30) cc_final: 0.7352 (m-30) outliers start: 26 outliers final: 5 residues processed: 295 average time/residue: 0.6386 time to fit residues: 217.1075 Evaluate side-chains 272 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 262 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2699 LEU Chi-restraints excluded: chain A residue 2861 GLN Chi-restraints excluded: chain A residue 3036 SER Chi-restraints excluded: chain A residue 3281 GLU Chi-restraints excluded: chain A residue 3583 THR Chi-restraints excluded: chain A residue 3980 SER Chi-restraints excluded: chain A residue 4029 SER Chi-restraints excluded: chain A residue 4039 GLN Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4645 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [25, 19, 177, 215, 141, 301, 300, 108, 185, 281, 294] chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 301 optimal weight: 6.9990 chunk 300 optimal weight: 0.9980 chunk 108 optimal weight: 50.0000 chunk 185 optimal weight: 5.9990 chunk 281 optimal weight: 0.7980 chunk 294 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS A1846 GLN A2110 GLN A2138 GLN A2235 GLN A2608 ASN A2826 GLN A3277 GLN A3669 ASN A3970 GLN A4588 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.193049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126820 restraints weight = 24066.272| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.07 r_work: 0.3216 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25046 Z= 0.202 Angle : 0.591 10.019 33955 Z= 0.298 Chirality : 0.042 0.169 3817 Planarity : 0.005 0.062 4327 Dihedral : 6.610 131.124 3318 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.72 % Allowed : 7.43 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 1.65 (0.15), residues: 3024 helix: 1.61 (0.12), residues: 1789 sheet: -0.45 (0.32), residues: 253 loop : 0.77 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2164 TYR 0.022 0.002 TYR A2828 PHE 0.027 0.002 PHE A3898 TRP 0.025 0.002 TRP A1605 HIS 0.009 0.001 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (25046) covalent geometry : angle 0.59144 / 0.30 (33955) hydrogen bonds : bond 0.04819 / 3.19 ( 1462) hydrogen bonds : angle 4.47815 / 3.33 ( 4254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 1547 ASN cc_start: 0.7625 (t0) cc_final: 0.7208 (t0) REVERT: A 1624 ASP cc_start: 0.7674 (m-30) cc_final: 0.7383 (m-30) REVERT: A 1670 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6986 (mt-10) REVERT: A 1723 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7448 (mmp-170) REVERT: A 1929 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.8006 (tpp) REVERT: A 2030 ARG cc_start: 0.7775 (mtt90) cc_final: 0.7529 (mtm180) REVERT: A 2122 GLU cc_start: 0.8061 (tt0) cc_final: 0.7428 (mp0) REVERT: A 2136 GLN cc_start: 0.8443 (tt0) cc_final: 0.8155 (tt0) REVERT: A 2338 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7146 (ttp80) REVERT: A 2358 ASP cc_start: 0.8392 (m-30) cc_final: 0.8095 (m-30) REVERT: A 2487 MET cc_start: 0.5149 (mmt) cc_final: 0.4886 (tpt) REVERT: A 2541 MET cc_start: 0.8859 (tpt) cc_final: 0.8586 (tpt) REVERT: A 2563 GLU cc_start: 0.7097 (tp30) cc_final: 0.6718 (tp30) REVERT: A 2628 LYS cc_start: 0.7640 (mttt) cc_final: 0.7427 (mtmt) REVERT: A 2630 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7384 (mtmm) REVERT: A 2721 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7566 (ttmm) REVERT: A 2861 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: A 2921 GLU cc_start: 0.7170 (pm20) cc_final: 0.6876 (pp20) REVERT: A 2948 ARG cc_start: 0.9082 (mmt-90) cc_final: 0.8854 (mpt-90) REVERT: A 2961 GLN cc_start: 0.8086 (pt0) cc_final: 0.7340 (pm20) REVERT: A 2970 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7230 (mt-10) REVERT: A 2975 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7577 (mmm-85) REVERT: A 3027 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7143 (mtp85) REVERT: A 3109 MET cc_start: 0.6171 (mmp) cc_final: 0.5715 (mpp) REVERT: A 3243 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 3281 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6232 (mt-10) REVERT: A 3583 THR cc_start: 0.6894 (OUTLIER) cc_final: 0.6505 (p) REVERT: A 3656 GLU cc_start: 0.7712 (tp30) cc_final: 0.7261 (tp30) REVERT: A 3767 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8360 (mtp180) REVERT: A 3800 GLU cc_start: 0.8031 (tp30) cc_final: 0.7282 (tt0) REVERT: A 3905 GLN cc_start: 0.7792 (mm110) cc_final: 0.6838 (pp30) REVERT: A 4039 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6999 (mt0) REVERT: A 4148 ASP cc_start: 0.6056 (t0) cc_final: 0.5733 (t0) REVERT: A 4372 ASP cc_start: 0.7629 (m-30) cc_final: 0.7369 (m-30) REVERT: A 4431 GLN cc_start: 0.7796 (tt0) cc_final: 0.7281 (tp-100) REVERT: A 4501 ARG cc_start: 0.7246 (ttt180) cc_final: 0.6600 (ttm170) REVERT: A 4548 LYS cc_start: 0.7500 (mptt) cc_final: 0.7277 (mptp) REVERT: A 4659 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8273 (mm) REVERT: A 4675 ASP cc_start: 0.7574 (m-30) cc_final: 0.7256 (m-30) outliers start: 47 outliers final: 21 residues processed: 283 average time/residue: 0.6531 time to fit residues: 212.3671 Evaluate side-chains 284 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1712 SER Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 1933 THR Chi-restraints excluded: chain A residue 2324 THR Chi-restraints excluded: chain A residue 2529 THR Chi-restraints excluded: chain A residue 2630 LYS Chi-restraints excluded: chain A residue 2653 THR Chi-restraints excluded: chain A residue 2699 LEU Chi-restraints excluded: chain A residue 2822 SER Chi-restraints excluded: chain A residue 2861 GLN Chi-restraints excluded: chain A residue 3036 SER Chi-restraints excluded: chain A residue 3243 ILE Chi-restraints excluded: chain A residue 3246 LEU Chi-restraints excluded: chain A residue 3281 GLU Chi-restraints excluded: chain A residue 3583 THR Chi-restraints excluded: chain A residue 3585 MET Chi-restraints excluded: chain A residue 3695 THR Chi-restraints excluded: chain A residue 3767 ARG Chi-restraints excluded: chain A residue 3882 VAL Chi-restraints excluded: chain A residue 3941 VAL Chi-restraints excluded: chain A residue 4029 SER Chi-restraints excluded: chain A residue 4039 GLN Chi-restraints excluded: chain A residue 4231 ARG Chi-restraints excluded: chain A residue 4258 THR Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4562 SER Chi-restraints excluded: chain A residue 4645 GLU Chi-restraints excluded: chain A residue 4659 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [284, 1, 300, 225, 267, 31, 253, 264, 21, 124, 19] chunk 284 optimal weight: 0.0770 chunk 1 optimal weight: 8.9990 chunk 300 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 267 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 264 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1596 ASN A1719 GLN A1846 GLN A2235 GLN A2608 ASN A2826 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.196048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127312 restraints weight = 23944.427| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.83 r_work: 0.3285 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25046 Z= 0.107 Angle : 0.496 9.624 33955 Z= 0.250 Chirality : 0.038 0.163 3817 Planarity : 0.004 0.050 4327 Dihedral : 6.151 116.289 3318 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.24 % Allowed : 9.15 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 1.99 (0.15), residues: 3024 helix: 1.90 (0.12), residues: 1779 sheet: -0.37 (0.33), residues: 246 loop : 0.89 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2731 TYR 0.019 0.001 TYR A3897 PHE 0.019 0.001 PHE A3898 TRP 0.025 0.001 TRP A2286 HIS 0.004 0.001 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (25046) covalent geometry : angle 0.49612 / 0.25 (33955) hydrogen bonds : bond 0.03885 / 2.57 ( 1462) hydrogen bonds : angle 4.23388 / 3.15 ( 4254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 1547 ASN cc_start: 0.7590 (t0) cc_final: 0.7188 (t0) REVERT: A 1624 ASP cc_start: 0.7641 (m-30) cc_final: 0.7343 (m-30) REVERT: A 1723 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7362 (mmp-170) REVERT: A 1776 GLU cc_start: 0.8887 (tp30) cc_final: 0.8546 (tp30) REVERT: A 2030 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7447 (mtm180) REVERT: A 2122 GLU cc_start: 0.7900 (tt0) cc_final: 0.7289 (mp0) REVERT: A 2136 GLN cc_start: 0.8320 (tt0) cc_final: 0.7936 (tt0) REVERT: A 2338 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7064 (ttp80) REVERT: A 2358 ASP cc_start: 0.8309 (m-30) cc_final: 0.7982 (m-30) REVERT: A 2440 ASP cc_start: 0.7297 (t0) cc_final: 0.6982 (t0) REVERT: A 2487 MET cc_start: 0.5170 (mmt) cc_final: 0.4906 (tpt) REVERT: A 2541 MET cc_start: 0.8754 (tpt) cc_final: 0.8460 (tpt) REVERT: A 2563 GLU cc_start: 0.6957 (tp30) cc_final: 0.6603 (tp30) REVERT: A 2721 LYS cc_start: 0.7834 (ttmt) cc_final: 0.7526 (ttmm) REVERT: A 2921 GLU cc_start: 0.7173 (pm20) cc_final: 0.6856 (pp20) REVERT: A 2943 LEU cc_start: 0.8363 (mm) cc_final: 0.8099 (mp) REVERT: A 2948 ARG cc_start: 0.9049 (mmt-90) cc_final: 0.8831 (mpt-90) REVERT: A 2961 GLN cc_start: 0.8072 (pt0) cc_final: 0.7334 (pm20) REVERT: A 2970 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 2975 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7574 (mmm-85) REVERT: A 3027 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7040 (mtp85) REVERT: A 3109 MET cc_start: 0.6219 (mmp) cc_final: 0.5742 (mpp) REVERT: A 3281 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6242 (mt-10) REVERT: A 3583 THR cc_start: 0.6796 (OUTLIER) cc_final: 0.6461 (p) REVERT: A 3656 GLU cc_start: 0.7548 (tp30) cc_final: 0.7118 (tp30) REVERT: A 3800 GLU cc_start: 0.8038 (tp30) cc_final: 0.7311 (tt0) REVERT: A 3905 GLN cc_start: 0.7722 (mm110) cc_final: 0.6784 (pp30) REVERT: A 4039 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.7024 (mt0) REVERT: A 4148 ASP cc_start: 0.5945 (t0) cc_final: 0.5613 (t0) REVERT: A 4372 ASP cc_start: 0.7601 (m-30) cc_final: 0.7332 (m-30) REVERT: A 4431 GLN cc_start: 0.7688 (tt0) cc_final: 0.7186 (tp-100) REVERT: A 4501 ARG cc_start: 0.7162 (ttt180) cc_final: 0.6574 (ttm110) REVERT: A 4548 LYS cc_start: 0.7362 (mptt) cc_final: 0.7144 (mptp) REVERT: A 4557 GLU cc_start: 0.7207 (mp0) cc_final: 0.7004 (mp0) REVERT: A 4580 GLU cc_start: 0.7657 (mp0) cc_final: 0.7413 (mp0) REVERT: A 4645 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: A 4675 ASP cc_start: 0.7581 (m-30) cc_final: 0.7271 (m-30) outliers start: 34 outliers final: 11 residues processed: 286 average time/residue: 0.6453 time to fit residues: 212.4769 Evaluate side-chains 265 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1933 THR Chi-restraints excluded: chain A residue 2699 LEU Chi-restraints excluded: chain A residue 2822 SER Chi-restraints excluded: chain A residue 3036 SER Chi-restraints excluded: chain A residue 3246 LEU Chi-restraints excluded: chain A residue 3281 GLU Chi-restraints excluded: chain A residue 3583 THR Chi-restraints excluded: chain A residue 3695 THR Chi-restraints excluded: chain A residue 3941 VAL Chi-restraints excluded: chain A residue 4029 SER Chi-restraints excluded: chain A residue 4039 GLN Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4401 GLU Chi-restraints excluded: chain A residue 4645 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [101, 36, 248, 121, 277, 117, 194, 31, 256, 61, 28] chunk 101 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 248 optimal weight: 0.2980 chunk 121 optimal weight: 0.8980 chunk 277 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1719 GLN A1846 GLN A1931 ASN A2235 GLN A2608 ASN A2826 GLN A3926 ASN ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.196552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130114 restraints weight = 24020.781| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.96 r_work: 0.3280 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25046 Z= 0.105 Angle : 0.491 10.744 33955 Z= 0.245 Chirality : 0.038 0.161 3817 Planarity : 0.004 0.049 4327 Dihedral : 5.900 104.150 3318 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Rotamer: Outliers : 1.54 % Allowed : 9.88 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 2.08 (0.16), residues: 3024 helix: 2.00 (0.12), residues: 1780 sheet: -0.37 (0.32), residues: 255 loop : 0.89 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2731 TYR 0.017 0.001 TYR A3897 PHE 0.020 0.001 PHE A3898 TRP 0.023 0.001 TRP A2286 HIS 0.004 0.001 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (25046) covalent geometry : angle 0.49099 / 0.25 (33955) hydrogen bonds : bond 0.03737 / 2.47 ( 1462) hydrogen bonds : angle 4.13767 / 3.08 ( 4254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1547 ASN cc_start: 0.7621 (t0) cc_final: 0.7208 (t0) REVERT: A 1575 MET cc_start: 0.5349 (pp-130) cc_final: 0.5009 (ppp) REVERT: A 1624 ASP cc_start: 0.7662 (m-30) cc_final: 0.7363 (m-30) REVERT: A 1723 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7290 (tpt170) REVERT: A 1776 GLU cc_start: 0.8831 (tp30) cc_final: 0.8476 (tp30) REVERT: A 2030 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7472 (mtm180) REVERT: A 2052 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7754 (mm-30) REVERT: A 2122 GLU cc_start: 0.7901 (tt0) cc_final: 0.7283 (mp0) REVERT: A 2136 GLN cc_start: 0.8356 (tt0) cc_final: 0.8015 (tt0) REVERT: A 2338 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7153 (ttp80) REVERT: A 2358 ASP cc_start: 0.8346 (m-30) cc_final: 0.8037 (m-30) REVERT: A 2440 ASP cc_start: 0.7180 (t0) cc_final: 0.6879 (t0) REVERT: A 2487 MET cc_start: 0.5154 (mmt) cc_final: 0.4900 (tpt) REVERT: A 2541 MET cc_start: 0.8790 (tpt) cc_final: 0.8463 (tpt) REVERT: A 2721 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7509 (ttmm) REVERT: A 2861 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.6785 (tt0) REVERT: A 2919 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: A 2921 GLU cc_start: 0.7148 (pm20) cc_final: 0.6860 (pp20) REVERT: A 2948 ARG cc_start: 0.9051 (mmt-90) cc_final: 0.8836 (mpt-90) REVERT: A 2957 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7237 (p) REVERT: A 2970 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7253 (mt-10) REVERT: A 2975 ARG cc_start: 0.7932 (mmm160) cc_final: 0.7576 (mmm-85) REVERT: A 3027 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7099 (mtp85) REVERT: A 3109 MET cc_start: 0.6189 (mmp) cc_final: 0.5678 (mpp) REVERT: A 3281 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6269 (mt-10) REVERT: A 3583 THR cc_start: 0.6811 (OUTLIER) cc_final: 0.6465 (p) REVERT: A 3656 GLU cc_start: 0.7651 (tp30) cc_final: 0.7216 (tp30) REVERT: A 3800 GLU cc_start: 0.8097 (tp30) cc_final: 0.7324 (tt0) REVERT: A 3905 GLN cc_start: 0.7717 (mm110) cc_final: 0.6834 (pp30) REVERT: A 4039 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.7021 (mt0) REVERT: A 4148 ASP cc_start: 0.5834 (t0) cc_final: 0.5578 (t0) REVERT: A 4372 ASP cc_start: 0.7608 (m-30) cc_final: 0.7339 (m-30) REVERT: A 4431 GLN cc_start: 0.7752 (tt0) cc_final: 0.7258 (tp-100) REVERT: A 4501 ARG cc_start: 0.7218 (ttt180) cc_final: 0.6629 (ttm110) REVERT: A 4548 LYS cc_start: 0.7220 (mptt) cc_final: 0.6979 (mptp) REVERT: A 4580 GLU cc_start: 0.7607 (mp0) cc_final: 0.7378 (mp0) REVERT: A 4645 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8517 (mt-10) REVERT: A 4675 ASP cc_start: 0.7581 (m-30) cc_final: 0.7281 (m-30) outliers start: 42 outliers final: 14 residues processed: 291 average time/residue: 0.6587 time to fit residues: 220.2264 Evaluate side-chains 274 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1933 THR Chi-restraints excluded: chain A residue 2699 LEU Chi-restraints excluded: chain A residue 2822 SER Chi-restraints excluded: chain A residue 2861 GLN Chi-restraints excluded: chain A residue 2919 GLU Chi-restraints excluded: chain A residue 2957 THR Chi-restraints excluded: chain A residue 3036 SER Chi-restraints excluded: chain A residue 3246 LEU Chi-restraints excluded: chain A residue 3281 GLU Chi-restraints excluded: chain A residue 3583 THR Chi-restraints excluded: chain A residue 3695 THR Chi-restraints excluded: chain A residue 3941 VAL Chi-restraints excluded: chain A residue 3980 SER Chi-restraints excluded: chain A residue 4029 SER Chi-restraints excluded: chain A residue 4039 GLN Chi-restraints excluded: chain A residue 4151 LEU Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4401 GLU Chi-restraints excluded: chain A residue 4645 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [221, 54, 38, 16, 202, 104, 95, 153, 76, 48, 91] chunk 221 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1719 GLN A1846 GLN A2110 GLN A2235 GLN A2295 GLN A2608 ASN A2826 GLN ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.198544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132618 restraints weight = 24154.522| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.90 r_work: 0.3307 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25046 Z= 0.125 Angle : 0.510 11.089 33955 Z= 0.254 Chirality : 0.039 0.161 3817 Planarity : 0.004 0.051 4327 Dihedral : 5.871 97.444 3318 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Rotamer: Outliers : 1.39 % Allowed : 11.01 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 2.09 (0.16), residues: 3024 helix: 2.00 (0.12), residues: 1774 sheet: -0.41 (0.33), residues: 247 loop : 0.94 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2731 TYR 0.019 0.001 TYR A3897 PHE 0.021 0.002 PHE A3898 TRP 0.023 0.001 TRP A2286 HIS 0.005 0.001 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (25046) covalent geometry : angle 0.51010 / 0.25 (33955) hydrogen bonds : bond 0.03920 / 2.59 ( 1462) hydrogen bonds : angle 4.15774 / 3.09 ( 4254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1547 ASN cc_start: 0.7673 (t0) cc_final: 0.7291 (t0) REVERT: A 1624 ASP cc_start: 0.7720 (m-30) cc_final: 0.7423 (m-30) REVERT: A 1723 ARG cc_start: 0.7671 (mtm-85) cc_final: 0.7297 (tpt170) REVERT: A 1776 GLU cc_start: 0.8860 (tp30) cc_final: 0.8517 (tp30) REVERT: A 2030 ARG cc_start: 0.7775 (mtt90) cc_final: 0.7518 (mtm180) REVERT: A 2052 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7767 (mm-30) REVERT: A 2122 GLU cc_start: 0.7924 (tt0) cc_final: 0.7350 (mp0) REVERT: A 2186 ILE cc_start: 0.7669 (mp) cc_final: 0.7352 (mp) REVERT: A 2338 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7226 (ttp80) REVERT: A 2358 ASP cc_start: 0.8385 (m-30) cc_final: 0.8088 (m-30) REVERT: A 2440 ASP cc_start: 0.7323 (t0) cc_final: 0.7015 (t0) REVERT: A 2487 MET cc_start: 0.5202 (mmt) cc_final: 0.4930 (tpt) REVERT: A 2541 MET cc_start: 0.8798 (tpt) cc_final: 0.8487 (tpt) REVERT: A 2721 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7564 (ttmm) REVERT: A 2861 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.6792 (tt0) REVERT: A 2921 GLU cc_start: 0.7157 (pm20) cc_final: 0.6864 (pp20) REVERT: A 2957 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.7182 (p) REVERT: A 2970 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7308 (mt-10) REVERT: A 2975 ARG cc_start: 0.7940 (mmm160) cc_final: 0.7591 (mmm-85) REVERT: A 3027 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7158 (mtp85) REVERT: A 3109 MET cc_start: 0.6246 (mmp) cc_final: 0.5722 (mpp) REVERT: A 3281 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6298 (mt-10) REVERT: A 3583 THR cc_start: 0.6808 (OUTLIER) cc_final: 0.6456 (p) REVERT: A 3656 GLU cc_start: 0.7649 (tp30) cc_final: 0.7228 (tp30) REVERT: A 3767 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8271 (mtp180) REVERT: A 3800 GLU cc_start: 0.8083 (tp30) cc_final: 0.7355 (tt0) REVERT: A 3905 GLN cc_start: 0.7724 (mm110) cc_final: 0.6918 (pp30) REVERT: A 4372 ASP cc_start: 0.7623 (m-30) cc_final: 0.7358 (m-30) REVERT: A 4431 GLN cc_start: 0.7787 (tt0) cc_final: 0.7273 (tp-100) REVERT: A 4501 ARG cc_start: 0.7182 (ttt180) cc_final: 0.6616 (ttm110) REVERT: A 4548 LYS cc_start: 0.7242 (mptt) cc_final: 0.6993 (mptp) REVERT: A 4645 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8499 (mt-10) REVERT: A 4675 ASP cc_start: 0.7647 (m-30) cc_final: 0.7350 (m-30) outliers start: 38 outliers final: 18 residues processed: 279 average time/residue: 0.6628 time to fit residues: 212.5536 Evaluate side-chains 274 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1933 THR Chi-restraints excluded: chain A residue 2214 LEU Chi-restraints excluded: chain A residue 2699 LEU Chi-restraints excluded: chain A residue 2822 SER Chi-restraints excluded: chain A residue 2861 GLN Chi-restraints excluded: chain A residue 2957 THR Chi-restraints excluded: chain A residue 3036 SER Chi-restraints excluded: chain A residue 3246 LEU Chi-restraints excluded: chain A residue 3281 GLU Chi-restraints excluded: chain A residue 3583 THR Chi-restraints excluded: chain A residue 3624 VAL Chi-restraints excluded: chain A residue 3695 THR Chi-restraints excluded: chain A residue 3767 ARG Chi-restraints excluded: chain A residue 3941 VAL Chi-restraints excluded: chain A residue 3980 SER Chi-restraints excluded: chain A residue 4029 SER Chi-restraints excluded: chain A residue 4151 LEU Chi-restraints excluded: chain A residue 4258 THR Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4401 GLU Chi-restraints excluded: chain A residue 4607 SER Chi-restraints excluded: chain A residue 4645 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [234, 243, 144, 164, 235, 67, 273, 72, 172, 29, 225] chunk 234 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 273 optimal weight: 0.0670 chunk 72 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 225 optimal weight: 9.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1719 GLN A1846 GLN A2235 GLN A2608 ASN A2656 HIS A2826 GLN ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.200132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135693 restraints weight = 24183.523| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.90 r_work: 0.3348 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25046 Z= 0.102 Angle : 0.490 11.044 33955 Z= 0.243 Chirality : 0.038 0.160 3817 Planarity : 0.004 0.049 4327 Dihedral : 5.634 92.397 3318 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.72 % Favored : 98.25 % Rotamer: Outliers : 1.24 % Allowed : 11.56 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 2.20 (0.16), residues: 3024 helix: 2.11 (0.12), residues: 1775 sheet: -0.36 (0.32), residues: 255 loop : 0.95 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2731 TYR 0.017 0.001 TYR A3897 PHE 0.018 0.001 PHE A3898 TRP 0.024 0.001 TRP A2286 HIS 0.004 0.000 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (25046) covalent geometry : angle 0.49047 / 0.24 (33955) hydrogen bonds : bond 0.03627 / 2.40 ( 1462) hydrogen bonds : angle 4.06551 / 3.03 ( 4254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1547 ASN cc_start: 0.7675 (t0) cc_final: 0.7307 (t0) REVERT: A 1624 ASP cc_start: 0.7710 (m-30) cc_final: 0.7429 (m-30) REVERT: A 1723 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7291 (mmm160) REVERT: A 1776 GLU cc_start: 0.8784 (tp30) cc_final: 0.8444 (tp30) REVERT: A 2030 ARG cc_start: 0.7762 (mtt90) cc_final: 0.7512 (mtm180) REVERT: A 2052 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7817 (mm-30) REVERT: A 2122 GLU cc_start: 0.7879 (tt0) cc_final: 0.7305 (mp0) REVERT: A 2338 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7317 (ttp80) REVERT: A 2358 ASP cc_start: 0.8355 (m-30) cc_final: 0.8049 (m-30) REVERT: A 2440 ASP cc_start: 0.7241 (t0) cc_final: 0.6927 (t0) REVERT: A 2487 MET cc_start: 0.5102 (mmt) cc_final: 0.4896 (tpt) REVERT: A 2541 MET cc_start: 0.8776 (tpt) cc_final: 0.8456 (tpt) REVERT: A 2721 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7544 (ttmm) REVERT: A 2861 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6763 (tt0) REVERT: A 2919 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: A 2921 GLU cc_start: 0.7109 (pm20) cc_final: 0.6857 (pp20) REVERT: A 2957 THR cc_start: 0.7454 (OUTLIER) cc_final: 0.7248 (p) REVERT: A 2970 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 3027 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7155 (mtp85) REVERT: A 3109 MET cc_start: 0.6241 (mmp) cc_final: 0.5710 (mpp) REVERT: A 3281 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6308 (mt-10) REVERT: A 3583 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.6460 (p) REVERT: A 3656 GLU cc_start: 0.7590 (tp30) cc_final: 0.7172 (tp30) REVERT: A 3800 GLU cc_start: 0.8035 (tp30) cc_final: 0.7311 (tt0) REVERT: A 3905 GLN cc_start: 0.7601 (mm110) cc_final: 0.6884 (pp30) REVERT: A 4372 ASP cc_start: 0.7635 (m-30) cc_final: 0.7380 (m-30) REVERT: A 4431 GLN cc_start: 0.7759 (tt0) cc_final: 0.7264 (tp-100) REVERT: A 4501 ARG cc_start: 0.7135 (ttt180) cc_final: 0.6581 (ttm110) REVERT: A 4645 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: A 4675 ASP cc_start: 0.7665 (m-30) cc_final: 0.7374 (m-30) outliers start: 34 outliers final: 18 residues processed: 282 average time/residue: 0.6476 time to fit residues: 211.2201 Evaluate side-chains 277 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1933 THR Chi-restraints excluded: chain A residue 2603 THR Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2699 LEU Chi-restraints excluded: chain A residue 2822 SER Chi-restraints excluded: chain A residue 2861 GLN Chi-restraints excluded: chain A residue 2919 GLU Chi-restraints excluded: chain A residue 2957 THR Chi-restraints excluded: chain A residue 3036 SER Chi-restraints excluded: chain A residue 3246 LEU Chi-restraints excluded: chain A residue 3281 GLU Chi-restraints excluded: chain A residue 3583 THR Chi-restraints excluded: chain A residue 3636 SER Chi-restraints excluded: chain A residue 3695 THR Chi-restraints excluded: chain A residue 3941 VAL Chi-restraints excluded: chain A residue 3980 SER Chi-restraints excluded: chain A residue 4029 SER Chi-restraints excluded: chain A residue 4151 LEU Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4401 GLU Chi-restraints excluded: chain A residue 4607 SER Chi-restraints excluded: chain A residue 4645 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [219, 126, 114, 195, 300, 22, 38, 230, 204, 65, 261] chunk 219 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 300 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1719 GLN A1846 GLN A2110 GLN A2235 GLN A2608 ASN A2826 GLN ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.197729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135250 restraints weight = 24193.621| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.07 r_work: 0.3323 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25046 Z= 0.142 Angle : 0.531 11.356 33955 Z= 0.264 Chirality : 0.039 0.161 3817 Planarity : 0.004 0.052 4327 Dihedral : 5.772 91.780 3318 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Rotamer: Outliers : 1.39 % Allowed : 11.96 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 2.05 (0.15), residues: 3024 helix: 1.98 (0.12), residues: 1777 sheet: -0.38 (0.32), residues: 262 loop : 0.89 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2164 TYR 0.020 0.002 TYR A2828 PHE 0.022 0.002 PHE A3898 TRP 0.022 0.001 TRP A2286 HIS 0.006 0.001 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (25046) covalent geometry : angle 0.53127 / 0.26 (33955) hydrogen bonds : bond 0.04048 / 2.68 ( 1462) hydrogen bonds : angle 4.17127 / 3.10 ( 4254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 1547 ASN cc_start: 0.7747 (t0) cc_final: 0.7369 (t0) REVERT: A 1624 ASP cc_start: 0.7761 (m-30) cc_final: 0.7485 (m-30) REVERT: A 1723 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7311 (tpt170) REVERT: A 1776 GLU cc_start: 0.8909 (tp30) cc_final: 0.8561 (tp30) REVERT: A 2030 ARG cc_start: 0.7738 (mtt90) cc_final: 0.7484 (mtm180) REVERT: A 2122 GLU cc_start: 0.7995 (tt0) cc_final: 0.7408 (mp0) REVERT: A 2186 ILE cc_start: 0.7681 (mp) cc_final: 0.7394 (mp) REVERT: A 2338 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7347 (ttp80) REVERT: A 2358 ASP cc_start: 0.8434 (m-30) cc_final: 0.8142 (m-30) REVERT: A 2440 ASP cc_start: 0.7446 (t0) cc_final: 0.7149 (t0) REVERT: A 2541 MET cc_start: 0.8831 (tpt) cc_final: 0.8530 (tpt) REVERT: A 2630 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7498 (mtmm) REVERT: A 2721 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7611 (ttmm) REVERT: A 2861 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.6790 (tt0) REVERT: A 2919 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: A 2921 GLU cc_start: 0.7132 (pm20) cc_final: 0.6868 (pp20) REVERT: A 2957 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.7110 (p) REVERT: A 2961 GLN cc_start: 0.8037 (pt0) cc_final: 0.7598 (tt0) REVERT: A 2970 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 2975 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7069 (mmm-85) REVERT: A 3027 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7178 (mtp85) REVERT: A 3109 MET cc_start: 0.6222 (mmp) cc_final: 0.5694 (mpp) REVERT: A 3147 MET cc_start: 0.9012 (mtt) cc_final: 0.8791 (mmm) REVERT: A 3196 ASN cc_start: 0.7760 (t0) cc_final: 0.7454 (t0) REVERT: A 3281 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6200 (mt-10) REVERT: A 3583 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.6443 (p) REVERT: A 3656 GLU cc_start: 0.7679 (tp30) cc_final: 0.7253 (tp30) REVERT: A 3767 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8323 (mtp180) REVERT: A 3800 GLU cc_start: 0.8103 (tp30) cc_final: 0.7374 (tt0) REVERT: A 3905 GLN cc_start: 0.7711 (mm110) cc_final: 0.6888 (pp30) REVERT: A 4372 ASP cc_start: 0.7635 (m-30) cc_final: 0.7369 (m-30) REVERT: A 4431 GLN cc_start: 0.7784 (tt0) cc_final: 0.7287 (tp-100) REVERT: A 4501 ARG cc_start: 0.7230 (ttt180) cc_final: 0.6662 (ttm110) REVERT: A 4645 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8531 (mt-10) REVERT: A 4675 ASP cc_start: 0.7671 (m-30) cc_final: 0.7424 (m-30) outliers start: 38 outliers final: 20 residues processed: 278 average time/residue: 0.6430 time to fit residues: 206.5608 Evaluate side-chains 283 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1931 ASN Chi-restraints excluded: chain A residue 1933 THR Chi-restraints excluded: chain A residue 2319 SER Chi-restraints excluded: chain A residue 2603 THR Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2630 LYS Chi-restraints excluded: chain A residue 2699 LEU Chi-restraints excluded: chain A residue 2822 SER Chi-restraints excluded: chain A residue 2861 GLN Chi-restraints excluded: chain A residue 2919 GLU Chi-restraints excluded: chain A residue 2957 THR Chi-restraints excluded: chain A residue 3036 SER Chi-restraints excluded: chain A residue 3246 LEU Chi-restraints excluded: chain A residue 3281 GLU Chi-restraints excluded: chain A residue 3583 THR Chi-restraints excluded: chain A residue 3636 SER Chi-restraints excluded: chain A residue 3695 THR Chi-restraints excluded: chain A residue 3767 ARG Chi-restraints excluded: chain A residue 3941 VAL Chi-restraints excluded: chain A residue 3980 SER Chi-restraints excluded: chain A residue 4029 SER Chi-restraints excluded: chain A residue 4151 LEU Chi-restraints excluded: chain A residue 4258 THR Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4401 GLU Chi-restraints excluded: chain A residue 4645 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [111, 224, 46, 9, 144, 258, 245, 274, 187, 45, 132] chunk 111 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 258 optimal weight: 0.0970 chunk 245 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 187 optimal weight: 0.0870 chunk 45 optimal weight: 0.0870 chunk 132 optimal weight: 1.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1719 GLN A1846 GLN A2235 GLN A2608 ASN A2826 GLN ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.200133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138420 restraints weight = 24429.045| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.91 r_work: 0.3346 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25046 Z= 0.095 Angle : 0.487 11.276 33955 Z= 0.242 Chirality : 0.038 0.160 3817 Planarity : 0.004 0.049 4327 Dihedral : 5.538 86.096 3318 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.65 % Favored : 98.31 % Rotamer: Outliers : 0.99 % Allowed : 12.55 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 2.26 (0.16), residues: 3024 helix: 2.17 (0.12), residues: 1775 sheet: -0.35 (0.33), residues: 255 loop : 0.96 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3086 TYR 0.016 0.001 TYR A3897 PHE 0.018 0.001 PHE A3898 TRP 0.026 0.001 TRP A2286 HIS 0.003 0.000 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.10 (25046) covalent geometry : angle 0.48659 / 0.24 (33955) hydrogen bonds : bond 0.03510 / 2.32 ( 1462) hydrogen bonds : angle 4.03788 / 3.00 ( 4254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 261 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 1547 ASN cc_start: 0.7702 (t0) cc_final: 0.7326 (t0) REVERT: A 1624 ASP cc_start: 0.7674 (m-30) cc_final: 0.7389 (m-30) REVERT: A 1723 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.7302 (mmm160) REVERT: A 2030 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7520 (mtm180) REVERT: A 2052 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7829 (mm-30) REVERT: A 2122 GLU cc_start: 0.7900 (tt0) cc_final: 0.7326 (mp0) REVERT: A 2186 ILE cc_start: 0.7662 (mp) cc_final: 0.7356 (mp) REVERT: A 2338 ARG cc_start: 0.7828 (ttm110) cc_final: 0.7371 (ttp80) REVERT: A 2358 ASP cc_start: 0.8381 (m-30) cc_final: 0.8060 (m-30) REVERT: A 2440 ASP cc_start: 0.7231 (t0) cc_final: 0.6921 (t0) REVERT: A 2541 MET cc_start: 0.8807 (tpt) cc_final: 0.8499 (tpt) REVERT: A 2721 LYS cc_start: 0.7791 (ttmt) cc_final: 0.7570 (ttmm) REVERT: A 2861 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.6775 (tt0) REVERT: A 2919 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: A 2921 GLU cc_start: 0.7061 (pm20) cc_final: 0.6810 (pp20) REVERT: A 2961 GLN cc_start: 0.8031 (pt0) cc_final: 0.7347 (pm20) REVERT: A 2970 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 3027 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7194 (mtp85) REVERT: A 3109 MET cc_start: 0.6300 (mmp) cc_final: 0.5773 (mpp) REVERT: A 3281 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6232 (mt-10) REVERT: A 3583 THR cc_start: 0.6737 (OUTLIER) cc_final: 0.6427 (p) REVERT: A 3656 GLU cc_start: 0.7641 (tp30) cc_final: 0.7220 (tp30) REVERT: A 3800 GLU cc_start: 0.8080 (tp30) cc_final: 0.7315 (tt0) REVERT: A 3905 GLN cc_start: 0.7674 (mm110) cc_final: 0.6911 (pp30) REVERT: A 4148 ASP cc_start: 0.6030 (t0) cc_final: 0.5818 (t0) REVERT: A 4372 ASP cc_start: 0.7622 (m-30) cc_final: 0.7361 (m-30) REVERT: A 4431 GLN cc_start: 0.7773 (tt0) cc_final: 0.7283 (tp-100) REVERT: A 4501 ARG cc_start: 0.7180 (ttt180) cc_final: 0.6612 (ttm110) REVERT: A 4508 LYS cc_start: 0.7346 (mtpp) cc_final: 0.6864 (mttp) REVERT: A 4645 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8465 (mp0) REVERT: A 4675 ASP cc_start: 0.7638 (m-30) cc_final: 0.7343 (m-30) outliers start: 27 outliers final: 16 residues processed: 278 average time/residue: 0.6539 time to fit residues: 209.8243 Evaluate side-chains 272 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1933 THR Chi-restraints excluded: chain A residue 2319 SER Chi-restraints excluded: chain A residue 2603 THR Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2699 LEU Chi-restraints excluded: chain A residue 2822 SER Chi-restraints excluded: chain A residue 2861 GLN Chi-restraints excluded: chain A residue 2919 GLU Chi-restraints excluded: chain A residue 3036 SER Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3246 LEU Chi-restraints excluded: chain A residue 3281 GLU Chi-restraints excluded: chain A residue 3583 THR Chi-restraints excluded: chain A residue 3695 THR Chi-restraints excluded: chain A residue 3941 VAL Chi-restraints excluded: chain A residue 3980 SER Chi-restraints excluded: chain A residue 4365 THR Chi-restraints excluded: chain A residue 4401 GLU Chi-restraints excluded: chain A residue 4645 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [139, 59, 243, 126, 255, 141, 36, 107, 270, 100, 269] chunk 139 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 243 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 269 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1846 GLN A1962 GLN A2110 GLN A2235 GLN A2608 ASN A2826 GLN A2891 GLN A3926 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.200127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138675 restraints weight = 24542.654| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.07 r_work: 0.3409 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25046 Z= 0.099 Angle : 0.493 11.447 33955 Z= 0.244 Chirality : 0.038 0.158 3817 Planarity : 0.004 0.048 4327 Dihedral : 5.422 82.843 3318 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 1.06 % Allowed : 12.55 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 2.30 (0.16), residues: 3024 helix: 2.19 (0.12), residues: 1776 sheet: -0.29 (0.33), residues: 255 loop : 0.98 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3086 TYR 0.017 0.001 TYR A2828 PHE 0.018 0.001 PHE A3898 TRP 0.025 0.001 TRP A2286 HIS 0.004 0.001 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (25046) covalent geometry : angle 0.49288 / 0.24 (33955) hydrogen bonds : bond 0.03519 / 2.32 ( 1462) hydrogen bonds : angle 4.00243 / 2.98 ( 4254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 0.895 Fit side-chains REVERT: A 1547 ASN cc_start: 0.7703 (t0) cc_final: 0.7341 (t0) REVERT: A 1624 ASP cc_start: 0.7683 (m-30) cc_final: 0.7397 (m-30) REVERT: A 1670 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7091 (mt-10) REVERT: A 1723 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7320 (mmm160) REVERT: A 2030 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7568 (mtm180) REVERT: A 2052 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7843 (mm-30) REVERT: A 2186 ILE cc_start: 0.7648 (mp) cc_final: 0.7333 (mp) REVERT: A 2338 ARG cc_start: 0.7866 (ttm110) cc_final: 0.7396 (ttp80) REVERT: A 2358 ASP cc_start: 0.8365 (m-30) cc_final: 0.8055 (m-30) REVERT: A 2440 ASP cc_start: 0.7197 (t0) cc_final: 0.6906 (t0) REVERT: A 2541 MET cc_start: 0.8802 (tpt) cc_final: 0.8526 (tpt) REVERT: A 2721 LYS cc_start: 0.7804 (ttmt) cc_final: 0.7585 (ttmm) REVERT: A 2861 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.6736 (tt0) REVERT: A 2921 GLU cc_start: 0.7082 (pm20) cc_final: 0.6829 (pp20) REVERT: A 2957 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.7092 (p) REVERT: A 2961 GLN cc_start: 0.8038 (pt0) cc_final: 0.7650 (tt0) REVERT: A 2970 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 2975 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7823 (mmm-85) REVERT: A 3027 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7218 (mtp85) REVERT: A 3109 MET cc_start: 0.6276 (mmp) cc_final: 0.5713 (mpp) REVERT: A 3281 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6276 (mt-10) REVERT: A 3583 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6467 (p) REVERT: A 3656 GLU cc_start: 0.7675 (tp30) cc_final: 0.7322 (tp30) REVERT: A 3735 ASN cc_start: 0.6946 (m-40) cc_final: 0.6489 (m110) REVERT: A 3800 GLU cc_start: 0.8116 (tp30) cc_final: 0.7373 (tt0) REVERT: A 4148 ASP cc_start: 0.6032 (t0) cc_final: 0.5821 (t0) REVERT: A 4372 ASP cc_start: 0.7625 (m-30) cc_final: 0.7373 (m-30) REVERT: A 4431 GLN cc_start: 0.7773 (tt0) cc_final: 0.7306 (tp-100) REVERT: A 4501 ARG cc_start: 0.7182 (ttt180) cc_final: 0.6656 (ttm110) REVERT: A 4508 LYS cc_start: 0.7374 (mtpp) cc_final: 0.6900 (mttp) REVERT: A 4645 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8492 (mp0) outliers start: 29 outliers final: 16 residues processed: 275 average time/residue: 0.6499 time to fit residues: 206.6466 Evaluate side-chains 275 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1933 THR Chi-restraints excluded: chain A residue 2319 SER Chi-restraints excluded: chain A residue 2603 THR Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2621 ASP Chi-restraints excluded: chain A residue 2699 LEU Chi-restraints excluded: chain A residue 2822 SER Chi-restraints excluded: chain A residue 2861 GLN Chi-restraints excluded: chain A residue 2957 THR Chi-restraints excluded: chain A residue 3036 SER Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3246 LEU Chi-restraints excluded: chain A residue 3281 GLU Chi-restraints excluded: chain A residue 3583 THR Chi-restraints excluded: chain A residue 3695 THR Chi-restraints excluded: chain A residue 3941 VAL Chi-restraints excluded: chain A residue 3980 SER Chi-restraints excluded: chain A residue 4401 GLU Chi-restraints excluded: chain A residue 4645 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: [89, 75, 183, 180, 198, 225, 60, 285, 129, 296, 23] chunk 89 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 129 optimal weight: 0.0000 chunk 296 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1846 GLN A2110 GLN A2235 GLN A2608 ASN A2826 GLN A2891 GLN A3905 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.199923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133338 restraints weight = 24215.838| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.82 r_work: 0.3337 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25046 Z= 0.111 Angle : 0.505 11.012 33955 Z= 0.248 Chirality : 0.038 0.157 3817 Planarity : 0.004 0.049 4327 Dihedral : 5.452 82.927 3318 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.69 % Favored : 98.28 % Rotamer: Outliers : 0.95 % Allowed : 12.81 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: 2.28 (0.16), residues: 3024 helix: 2.16 (0.12), residues: 1777 sheet: -0.29 (0.32), residues: 255 loop : 0.98 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3086 TYR 0.018 0.001 TYR A2828 PHE 0.019 0.001 PHE A3898 TRP 0.023 0.001 TRP A2286 HIS 0.004 0.001 HIS A1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (25046) covalent geometry : angle 0.50476 / 0.25 (33955) hydrogen bonds : bond 0.03606 / 2.38 ( 1462) hydrogen bonds : angle 4.02106 / 2.99 ( 4254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10439.71 seconds wall clock time: 177 minutes 43.65 seconds (10663.65 seconds total)