Starting phenix.real_space_refine on Fri Dec 27 06:33:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dyv_27783/12_2024/8dyv_27783_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dyv_27783/12_2024/8dyv_27783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dyv_27783/12_2024/8dyv_27783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dyv_27783/12_2024/8dyv_27783.map" model { file = "/net/cci-nas-00/data/ceres_data/8dyv_27783/12_2024/8dyv_27783_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dyv_27783/12_2024/8dyv_27783_neut_trim.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 S 127 5.16 5 C 14657 2.51 5 N 3986 2.21 5 O 4273 1.98 5 H 22874 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 45926 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 41027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2549, 41027 Classifications: {'peptide': 2549} Link IDs: {'PCIS': 2, 'PTRANS': 120, 'TRANS': 2426} Chain breaks: 18 Chain: "B" Number of atoms: 4787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 4787 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 294} Chain breaks: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 15.77, per 1000 atoms: 0.34 Number of scatterers: 45926 At special positions: 0 Unit cell: (104.4, 155.44, 170.52, 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 127 16.00 P 9 15.00 O 4273 8.00 N 3986 7.00 C 14657 6.00 H 22874 1.00 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: 9.36 Conformation dependent library (CDL) restraints added in 2.6 seconds 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5432 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 26 sheets defined 55.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 1705 through 1730 removed outlier: 4.840A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 4.808A pdb=" N THR A1740 " --> pdb=" O ASN A1736 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1768 Processing helix chain 'A' and resid 1776 through 1796 Processing helix chain 'A' and resid 1804 through 1828 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1963 through 1987 removed outlier: 4.036A pdb=" N MET A1967 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A1971 " --> pdb=" O MET A1967 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2111 Processing helix chain 'A' and resid 2133 through 2145 Processing helix chain 'A' and resid 2150 through 2152 No H-bonds generated for 'chain 'A' and resid 2150 through 2152' Processing helix chain 'A' and resid 2153 through 2165 removed outlier: 3.553A pdb=" N LEU A2157 " --> pdb=" O ASP A2153 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A2159 " --> pdb=" O PRO A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2215 removed outlier: 3.587A pdb=" N VAL A2204 " --> pdb=" O GLY A2200 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN A2215 " --> pdb=" O TYR A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 Processing helix chain 'A' and resid 2308 through 2313 Processing helix chain 'A' and resid 2314 through 2316 No H-bonds generated for 'chain 'A' and resid 2314 through 2316' Processing helix chain 'A' and resid 2352 through 2359 removed outlier: 4.223A pdb=" N CYS A2359 " --> pdb=" O THR A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.533A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2424 Processing helix chain 'A' and resid 2432 through 2441 removed outlier: 3.894A pdb=" N PHE A2441 " --> pdb=" O LEU A2437 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.560A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 4.191A pdb=" N ARG A2488 " --> pdb=" O GLU A2484 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A2503 " --> pdb=" O LEU A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 removed outlier: 3.619A pdb=" N VAL A2552 " --> pdb=" O GLN A2549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2549 through 2552' Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 4.152A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 4.037A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2610 removed outlier: 3.598A pdb=" N ARG A2610 " --> pdb=" O PHE A2606 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.219A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A2634 " --> pdb=" O LEU A2630 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 removed outlier: 3.501A pdb=" N HIS A2689 " --> pdb=" O GLN A2685 " (cutoff:3.500A) Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2739 through 2756 removed outlier: 4.056A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 4.288A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2782 removed outlier: 3.526A pdb=" N LEU A2769 " --> pdb=" O TYR A2765 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A2777 " --> pdb=" O MET A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2796 through 2811 removed outlier: 3.574A pdb=" N ARG A2801 " --> pdb=" O ARG A2797 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2833 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.559A pdb=" N LEU A2889 " --> pdb=" O ASP A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.731A pdb=" N LEU A2916 " --> pdb=" O PHE A2912 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A2917 " --> pdb=" O ASN A2913 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2986 Processing helix chain 'A' and resid 2995 through 2999 Processing helix chain 'A' and resid 3001 through 3015 Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3062 removed outlier: 3.595A pdb=" N LEU A3062 " --> pdb=" O VAL A3058 " (cutoff:3.500A) Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3087 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 removed outlier: 3.965A pdb=" N HIS A3151 " --> pdb=" O CYS A3147 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A3156 " --> pdb=" O GLN A3152 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3214 removed outlier: 3.622A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3474 through 3495 removed outlier: 4.621A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A3495 " --> pdb=" O LYS A3491 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3502 removed outlier: 3.929A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3580 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.768A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3693 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3754 Processing helix chain 'A' and resid 3763 through 3801 removed outlier: 3.801A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A3770 " --> pdb=" O ILE A3766 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A3772 " --> pdb=" O THR A3768 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A3780 " --> pdb=" O GLU A3776 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A3783 " --> pdb=" O GLU A3779 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP A3788 " --> pdb=" O VAL A3784 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A3789 " --> pdb=" O GLU A3785 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A3792 " --> pdb=" O ASP A3788 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A3793 " --> pdb=" O ILE A3789 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A3795 " --> pdb=" O MET A3791 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A3796 " --> pdb=" O GLN A3792 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A3797 " --> pdb=" O GLU A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3817 removed outlier: 3.912A pdb=" N SER A3805 " --> pdb=" O TYR A3801 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3821 Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.854A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.843A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3890 removed outlier: 3.810A pdb=" N ALA A3884 " --> pdb=" O HIS A3880 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A3890 " --> pdb=" O LEU A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3901 through 3906 Processing helix chain 'A' and resid 3906 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 removed outlier: 4.317A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3954 through 3962 removed outlier: 3.980A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 removed outlier: 3.501A pdb=" N HIS A4006 " --> pdb=" O LEU A4002 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A4007 " --> pdb=" O ALA A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4015 through 4018 removed outlier: 4.063A pdb=" N MET A4018 " --> pdb=" O GLU A4015 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4015 through 4018' Processing helix chain 'A' and resid 4026 through 4035 Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.632A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 Processing helix chain 'A' and resid 4098 through 4101 removed outlier: 3.808A pdb=" N LEU A4101 " --> pdb=" O ASN A4098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4098 through 4101' Processing helix chain 'A' and resid 4102 through 4114 Processing helix chain 'A' and resid 4135 through 4142 removed outlier: 3.620A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4151 through 4164 removed outlier: 4.185A pdb=" N ALA A4155 " --> pdb=" O PRO A4151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A4156 " --> pdb=" O GLY A4152 " (cutoff:3.500A) Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.511A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4173 through 4194 removed outlier: 4.379A pdb=" N ALA A4177 " --> pdb=" O PRO A4173 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4195 through 4197 No H-bonds generated for 'chain 'A' and resid 4195 through 4197' Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.538A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A4227 " --> pdb=" O LEU A4223 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 removed outlier: 3.750A pdb=" N ILE A4238 " --> pdb=" O PRO A4235 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 removed outlier: 3.606A pdb=" N SER A4250 " --> pdb=" O LEU A4246 " (cutoff:3.500A) Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 4.763A pdb=" N GLN A4307 " --> pdb=" O GLU A4303 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4330 through 4347 removed outlier: 4.046A pdb=" N VAL A4337 " --> pdb=" O THR A4333 " (cutoff:3.500A) Processing helix chain 'A' and resid 4380 through 4389 removed outlier: 3.667A pdb=" N TRP A4387 " --> pdb=" O THR A4383 " (cutoff:3.500A) Processing helix chain 'A' and resid 4409 through 4440 Processing helix chain 'A' and resid 4445 through 4457 removed outlier: 3.763A pdb=" N LYS A4457 " --> pdb=" O ASN A4453 " (cutoff:3.500A) Processing helix chain 'A' and resid 4461 through 4465 Processing helix chain 'A' and resid 4474 through 4498 Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.550A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4633 through 4638 Processing helix chain 'B' and resid 287 through 297 removed outlier: 4.369A pdb=" N SER B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing sheet with id=AA1, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA2, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA3, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 5.801A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA5, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 6.529A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASP A2304 " --> pdb=" O HIS A2252 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A2254 " --> pdb=" O ASP A2304 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A2220 " --> pdb=" O PHE A2343 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A2345 " --> pdb=" O LEU A2220 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N MET A2222 " --> pdb=" O VAL A2345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA7, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA8, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AA9, first strand: chain 'A' and resid 2615 through 2619 removed outlier: 3.531A pdb=" N GLN A2707 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A2661 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 4.191A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.700A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2958 through 2960 removed outlier: 6.395A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 7.967A pdb=" N THR A3681 " --> pdb=" O PRO A3587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A3589 " --> pdb=" O THR A3681 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 Processing sheet with id=AB7, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 7.048A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N CYS A4286 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LYS A4292 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.411A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4564 through 4566 Processing sheet with id=AC1, first strand: chain 'A' and resid 4604 through 4607 Processing sheet with id=AC2, first strand: chain 'B' and resid 102 through 103 removed outlier: 4.824A pdb=" N TYR B 102 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 406 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 111 through 116 removed outlier: 4.351A pdb=" N THR B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 136 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 142 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 153 through 156 removed outlier: 6.934A pdb=" N CYS B 168 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 156 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA B 166 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 174 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR B 187 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 176 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 195 through 200 removed outlier: 3.640A pdb=" N SER B 197 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 237 through 242 Processing sheet with id=AC7, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.790A pdb=" N GLY B 314 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 282 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 312 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP B 284 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE B 310 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 320 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR B 333 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET B 322 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 341 through 346 removed outlier: 6.238A pdb=" N ASP B 366 " --> pdb=" O CYS B 372 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS B 372 " --> pdb=" O ASP B 366 " (cutoff:3.500A) 1228 hydrogen bonds defined for protein. 3558 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: 18.78 Time building geometry restraints manager: 11.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 22828 1.03 - 1.23: 411 1.23 - 1.43: 9452 1.43 - 1.63: 13535 1.63 - 1.82: 208 Bond restraints: 46434 Sorted by residual: bond pdb=" C LEU A2728 " pdb=" N ARG A2729 " ideal model delta sigma weight residual 1.335 1.210 0.125 1.36e-02 5.41e+03 8.45e+01 bond pdb=" C ARG A2729 " pdb=" N HIS A2730 " ideal model delta sigma weight residual 1.335 1.432 -0.097 1.38e-02 5.25e+03 4.93e+01 bond pdb=" C ASP A2835 " pdb=" O ASP A2835 " ideal model delta sigma weight residual 1.236 1.156 0.080 1.31e-02 5.83e+03 3.75e+01 bond pdb=" C ARG A4263 " pdb=" O ARG A4263 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.16e-02 7.43e+03 3.39e+01 bond pdb=" C VAL A2592 " pdb=" O VAL A2592 " ideal model delta sigma weight residual 1.238 1.175 0.063 1.10e-02 8.26e+03 3.28e+01 ... (remaining 46429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 82440 2.34 - 4.68: 1271 4.68 - 7.02: 164 7.02 - 9.36: 29 9.36 - 11.70: 12 Bond angle restraints: 83916 Sorted by residual: angle pdb=" CA ARG A4263 " pdb=" C ARG A4263 " pdb=" O ARG A4263 " ideal model delta sigma weight residual 120.70 111.22 9.48 1.03e+00 9.43e-01 8.47e+01 angle pdb=" CA ARG A3782 " pdb=" C ARG A3782 " pdb=" O ARG A3782 " ideal model delta sigma weight residual 120.82 112.10 8.72 1.05e+00 9.07e-01 6.90e+01 angle pdb=" CA LEU A2728 " pdb=" C LEU A2728 " pdb=" N ARG A2729 " ideal model delta sigma weight residual 117.63 127.41 -9.78 1.25e+00 6.40e-01 6.12e+01 angle pdb=" N MET A3791 " pdb=" CA MET A3791 " pdb=" C MET A3791 " ideal model delta sigma weight residual 111.82 103.07 8.75 1.16e+00 7.43e-01 5.69e+01 angle pdb=" CA TYR A4049 " pdb=" C TYR A4049 " pdb=" O TYR A4049 " ideal model delta sigma weight residual 120.32 112.02 8.30 1.11e+00 8.12e-01 5.59e+01 ... (remaining 83911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 21128 35.67 - 71.35: 635 71.35 - 107.02: 30 107.02 - 142.69: 1 142.69 - 178.36: 3 Dihedral angle restraints: 21797 sinusoidal: 11945 harmonic: 9852 Sorted by residual: dihedral pdb=" O1B ADP A4702 " pdb=" O3A ADP A4702 " pdb=" PB ADP A4702 " pdb=" PA ADP A4702 " ideal model delta sinusoidal sigma weight residual 300.00 121.63 178.36 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 109.28 -169.28 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' ADP A4702 " pdb=" O5' ADP A4702 " pdb=" PA ADP A4702 " pdb=" O2A ADP A4702 " ideal model delta sinusoidal sigma weight residual 300.00 151.07 148.93 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 21794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3311 0.087 - 0.173: 258 0.173 - 0.260: 18 0.260 - 0.347: 2 0.347 - 0.433: 1 Chirality restraints: 3590 Sorted by residual: chirality pdb=" CA PRO B 98 " pdb=" N PRO B 98 " pdb=" C PRO B 98 " pdb=" CB PRO B 98 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" C3' ATP A4703 " pdb=" C2' ATP A4703 " pdb=" C4' ATP A4703 " pdb=" O3' ATP A4703 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C2' ATP A4703 " pdb=" C1' ATP A4703 " pdb=" C3' ATP A4703 " pdb=" O2' ATP A4703 " both_signs ideal model delta sigma weight residual False -2.68 -2.95 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 3587 not shown) Planarity restraints: 6770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A3069 " -0.032 2.00e-02 2.50e+03 4.41e-01 2.92e+03 pdb=" CG ASN A3069 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN A3069 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A3069 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A3069 " 0.762 2.00e-02 2.50e+03 pdb="HD22 ASN A3069 " -0.765 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A3772 " 0.144 2.00e-02 2.50e+03 4.30e-01 2.77e+03 pdb=" CG ASN A3772 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A3772 " -0.138 2.00e-02 2.50e+03 pdb=" ND2 ASN A3772 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A3772 " 0.736 2.00e-02 2.50e+03 pdb="HD22 ASN A3772 " -0.725 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A3906 " 0.255 2.00e-02 2.50e+03 3.39e-01 1.72e+03 pdb=" CD GLN A3906 " -0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN A3906 " -0.244 2.00e-02 2.50e+03 pdb=" NE2 GLN A3906 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A3906 " -0.525 2.00e-02 2.50e+03 pdb="HE22 GLN A3906 " 0.536 2.00e-02 2.50e+03 ... (remaining 6767 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1270 2.15 - 2.76: 86755 2.76 - 3.37: 135456 3.37 - 3.99: 167858 3.99 - 4.60: 261311 Nonbonded interactions: 652650 Sorted by model distance: nonbonded pdb=" H ASN A1931 " pdb=" HG1 THR A2326 " model vdw 1.535 2.100 nonbonded pdb=" HD2 LYS A4505 " pdb=" HE2 TYR A4527 " model vdw 1.558 2.270 nonbonded pdb="HD21 ASN A2217 " pdb=" HA3 GLY A2360 " model vdw 1.628 2.270 nonbonded pdb=" OE1 GLU A2888 " pdb=" H GLU A2888 " model vdw 1.651 2.450 nonbonded pdb=" H THR A2944 " pdb=" O1B ADP A4704 " model vdw 1.656 2.450 ... (remaining 652645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.580 Extract box with map and model: 1.240 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 75.430 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 23560 Z= 0.322 Angle : 0.893 11.620 31952 Z= 0.532 Chirality : 0.046 0.433 3590 Planarity : 0.006 0.054 4070 Dihedral : 15.821 178.362 8784 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 0.20 % Allowed : 12.71 % Favored : 87.10 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2810 helix: 0.79 (0.14), residues: 1370 sheet: -0.63 (0.27), residues: 348 loop : -0.79 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A2584 HIS 0.012 0.001 HIS B 381 PHE 0.049 0.002 PHE A3021 TYR 0.025 0.002 TYR A3552 ARG 0.012 0.000 ARG A2720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 414 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8259 (tpp) cc_final: 0.7612 (tpp) REVERT: A 2349 LYS cc_start: 0.8781 (mttt) cc_final: 0.7851 (tptt) REVERT: A 2603 MET cc_start: 0.8512 (ttp) cc_final: 0.7589 (tmm) outliers start: 5 outliers final: 2 residues processed: 415 average time/residue: 0.7080 time to fit residues: 457.8587 Evaluate side-chains 387 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 3886 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2047 GLN A2067 ASN ** A2621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3792 GLN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4191 GLN ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4316 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23560 Z= 0.268 Angle : 0.610 8.599 31952 Z= 0.318 Chirality : 0.040 0.174 3590 Planarity : 0.005 0.046 4070 Dihedral : 7.923 159.822 3158 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 1.53 % Allowed : 13.73 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2810 helix: 0.77 (0.13), residues: 1403 sheet: -0.87 (0.27), residues: 371 loop : -0.78 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A2825 HIS 0.005 0.001 HIS A4100 PHE 0.014 0.002 PHE A2776 TYR 0.020 0.002 TYR A2496 ARG 0.011 0.000 ARG A2729 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 384 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7287 (tmm) cc_final: 0.7080 (tmm) REVERT: A 1877 ASP cc_start: 0.7805 (t0) cc_final: 0.7110 (p0) REVERT: A 2012 MET cc_start: 0.8619 (tmm) cc_final: 0.7967 (tmm) REVERT: A 2349 LYS cc_start: 0.8845 (mttt) cc_final: 0.7914 (tptt) REVERT: A 2603 MET cc_start: 0.8551 (ttp) cc_final: 0.8322 (ttp) REVERT: A 3195 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6677 (mm-30) REVERT: A 3906 GLN cc_start: 0.7177 (mm110) cc_final: 0.6105 (tt0) REVERT: A 4180 TYR cc_start: 0.8020 (m-80) cc_final: 0.7805 (m-80) REVERT: A 4465 SER cc_start: 0.8351 (m) cc_final: 0.7990 (t) REVERT: B 201 MET cc_start: 0.3453 (tpt) cc_final: 0.3238 (tpt) outliers start: 39 outliers final: 28 residues processed: 399 average time/residue: 0.6521 time to fit residues: 407.6525 Evaluate side-chains 382 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 353 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2269 ASP Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2584 TRP Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2621 ASN Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 3010 THR Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3089 CYS Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3634 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3776 GLU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4263 ARG Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4452 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 359 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN A2212 GLN A2827 HIS ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3907 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23560 Z= 0.244 Angle : 0.587 8.009 31952 Z= 0.304 Chirality : 0.039 0.170 3590 Planarity : 0.004 0.063 4070 Dihedral : 7.354 157.979 3158 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 2.20 % Allowed : 13.93 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2810 helix: 0.81 (0.14), residues: 1403 sheet: -1.00 (0.27), residues: 362 loop : -0.91 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A4534 HIS 0.006 0.001 HIS A4029 PHE 0.012 0.001 PHE A3738 TYR 0.019 0.001 TYR A2496 ARG 0.005 0.000 ARG A4615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 360 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.7309 (tmm) cc_final: 0.7075 (tmm) REVERT: A 1872 TYR cc_start: 0.6767 (t80) cc_final: 0.6561 (t80) REVERT: A 1877 ASP cc_start: 0.7813 (t0) cc_final: 0.7015 (p0) REVERT: A 1888 CYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8323 (m) REVERT: A 2012 MET cc_start: 0.8717 (tmm) cc_final: 0.7745 (tmm) REVERT: A 2349 LYS cc_start: 0.9008 (mttt) cc_final: 0.8064 (tptt) REVERT: A 2603 MET cc_start: 0.8379 (ttp) cc_final: 0.8154 (ttp) REVERT: A 3195 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: A 4465 SER cc_start: 0.8411 (m) cc_final: 0.8108 (t) REVERT: B 201 MET cc_start: 0.3882 (tpt) cc_final: 0.3675 (tpt) REVERT: B 381 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.7035 (t70) outliers start: 56 outliers final: 38 residues processed: 385 average time/residue: 0.6244 time to fit residues: 384.2023 Evaluate side-chains 385 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 344 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1888 CYS Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2664 ASP Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 3010 THR Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3634 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3838 ASN Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4030 ILE Chi-restraints excluded: chain A residue 4100 HIS Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4398 LEU Chi-restraints excluded: chain A residue 4452 ILE Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 381 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1931 ASN A2218 HIS A2713 ASN ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23560 Z= 0.348 Angle : 0.655 9.220 31952 Z= 0.347 Chirality : 0.041 0.161 3590 Planarity : 0.005 0.053 4070 Dihedral : 7.467 168.660 3158 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.52 % Rotamer: Outliers : 2.83 % Allowed : 15.70 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 2810 helix: 0.32 (0.13), residues: 1402 sheet: -1.20 (0.27), residues: 356 loop : -1.27 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2825 HIS 0.007 0.001 HIS A4397 PHE 0.016 0.002 PHE A2912 TYR 0.023 0.002 TYR A2496 ARG 0.006 0.000 ARG A2726 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 344 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1877 ASP cc_start: 0.7924 (t0) cc_final: 0.7033 (p0) REVERT: A 1888 CYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8318 (m) REVERT: A 2012 MET cc_start: 0.8795 (tmm) cc_final: 0.8040 (tmm) REVERT: A 2349 LYS cc_start: 0.9024 (mttt) cc_final: 0.8080 (tptt) REVERT: A 2953 MET cc_start: 0.7833 (ttt) cc_final: 0.7604 (ttt) REVERT: A 3020 LEU cc_start: 0.8465 (mt) cc_final: 0.8123 (pt) REVERT: A 3195 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6361 (mm-30) REVERT: A 3870 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6054 (mmt-90) REVERT: A 4033 THR cc_start: 0.8232 (t) cc_final: 0.7772 (p) REVERT: A 4095 MET cc_start: 0.7781 (tmm) cc_final: 0.7191 (ttp) REVERT: A 4465 SER cc_start: 0.8444 (m) cc_final: 0.8151 (t) REVERT: B 101 LYS cc_start: 0.5739 (OUTLIER) cc_final: 0.5322 (mmtm) REVERT: B 236 TRP cc_start: 0.5739 (OUTLIER) cc_final: 0.5169 (p90) outliers start: 72 outliers final: 52 residues processed: 389 average time/residue: 0.6557 time to fit residues: 411.3559 Evaluate side-chains 392 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 335 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1888 CYS Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2664 ASP Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2713 ASN Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2971 ASP Chi-restraints excluded: chain A residue 3010 THR Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3148 VAL Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3634 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3814 THR Chi-restraints excluded: chain A residue 3822 HIS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3860 THR Chi-restraints excluded: chain A residue 3870 ARG Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4030 ILE Chi-restraints excluded: chain A residue 4100 HIS Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4452 ILE Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 236 TRP Chi-restraints excluded: chain B residue 354 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 246 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23560 Z= 0.262 Angle : 0.600 8.793 31952 Z= 0.312 Chirality : 0.039 0.153 3590 Planarity : 0.005 0.055 4070 Dihedral : 7.239 176.015 3155 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 2.79 % Allowed : 16.33 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2810 helix: 0.51 (0.13), residues: 1404 sheet: -1.17 (0.27), residues: 347 loop : -1.26 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A4534 HIS 0.006 0.001 HIS A4397 PHE 0.016 0.002 PHE A3738 TYR 0.019 0.002 TYR A2496 ARG 0.005 0.000 ARG A2726 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 359 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1877 ASP cc_start: 0.7790 (t0) cc_final: 0.7061 (p0) REVERT: A 1888 CYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8283 (m) REVERT: A 2012 MET cc_start: 0.8800 (tmm) cc_final: 0.7954 (tmm) REVERT: A 3176 TYR cc_start: 0.7517 (t80) cc_final: 0.7284 (t80) REVERT: A 3195 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6523 (mm-30) REVERT: A 3500 MET cc_start: 0.8005 (mmm) cc_final: 0.7536 (mmm) REVERT: A 3543 PHE cc_start: 0.6881 (p90) cc_final: 0.6510 (p90) REVERT: A 4075 GLU cc_start: 0.7095 (tp30) cc_final: 0.6859 (tp30) REVERT: A 4095 MET cc_start: 0.7756 (tmm) cc_final: 0.7153 (ttp) REVERT: A 4465 SER cc_start: 0.8466 (m) cc_final: 0.8229 (t) REVERT: B 101 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5338 (mmtm) outliers start: 71 outliers final: 55 residues processed: 404 average time/residue: 0.6303 time to fit residues: 407.1878 Evaluate side-chains 405 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 347 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1888 CYS Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2359 CYS Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2475 ASN Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2621 ASN Chi-restraints excluded: chain A residue 2664 ASP Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2774 VAL Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2971 ASP Chi-restraints excluded: chain A residue 3021 PHE Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3089 CYS Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3148 VAL Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3634 LEU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3675 PHE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3822 HIS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4030 ILE Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4387 TRP Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4452 ILE Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 359 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 274 optimal weight: 9.9990 chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 144 optimal weight: 3.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23560 Z= 0.203 Angle : 0.568 8.835 31952 Z= 0.290 Chirality : 0.039 0.152 3590 Planarity : 0.004 0.057 4070 Dihedral : 6.984 177.146 3155 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.52 % Rotamer: Outliers : 2.40 % Allowed : 17.55 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2810 helix: 0.83 (0.14), residues: 1403 sheet: -1.12 (0.27), residues: 347 loop : -1.12 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A4534 HIS 0.006 0.001 HIS B 337 PHE 0.015 0.001 PHE A3738 TYR 0.017 0.001 TYR A3552 ARG 0.006 0.000 ARG A2726 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 364 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1877 ASP cc_start: 0.7716 (t0) cc_final: 0.7059 (p0) REVERT: A 1888 CYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8236 (m) REVERT: A 1960 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8354 (m-10) REVERT: A 2012 MET cc_start: 0.8788 (tmm) cc_final: 0.7901 (tmm) REVERT: A 2953 MET cc_start: 0.7761 (ttt) cc_final: 0.7510 (ttp) REVERT: A 3195 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6287 (mm-30) REVERT: A 3500 MET cc_start: 0.7988 (mmm) cc_final: 0.7696 (mmm) REVERT: A 3543 PHE cc_start: 0.6895 (p90) cc_final: 0.6603 (p90) REVERT: A 3870 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6077 (mmt-90) REVERT: A 4075 GLU cc_start: 0.6956 (tp30) cc_final: 0.6650 (tp30) REVERT: A 4095 MET cc_start: 0.7803 (tmm) cc_final: 0.7175 (ttp) REVERT: A 4465 SER cc_start: 0.8415 (m) cc_final: 0.8181 (t) outliers start: 61 outliers final: 47 residues processed: 404 average time/residue: 0.6211 time to fit residues: 401.5833 Evaluate side-chains 396 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 345 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1888 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2475 ASN Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2693 TYR Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2971 ASP Chi-restraints excluded: chain A residue 3021 PHE Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3148 VAL Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3675 PHE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3822 HIS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3870 ARG Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4030 ILE Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4387 TRP Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4452 ILE Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 359 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 10.0000 chunk 30 optimal weight: 0.0370 chunk 156 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 166 optimal weight: 0.0670 chunk 126 optimal weight: 5.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23560 Z= 0.173 Angle : 0.550 8.077 31952 Z= 0.278 Chirality : 0.039 0.159 3590 Planarity : 0.004 0.048 4070 Dihedral : 6.694 171.088 3155 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 2.36 % Allowed : 17.78 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2810 helix: 1.10 (0.14), residues: 1404 sheet: -1.03 (0.27), residues: 354 loop : -0.98 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A4534 HIS 0.007 0.001 HIS B 381 PHE 0.013 0.001 PHE A3738 TYR 0.019 0.001 TYR A3552 ARG 0.005 0.000 ARG A2726 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 362 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1846 PHE cc_start: 0.7776 (t80) cc_final: 0.7556 (t80) REVERT: A 1877 ASP cc_start: 0.7611 (t0) cc_final: 0.7018 (p0) REVERT: A 1888 CYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8218 (m) REVERT: A 1960 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8330 (m-10) REVERT: A 2012 MET cc_start: 0.8836 (tmm) cc_final: 0.7809 (tmm) REVERT: A 2175 MET cc_start: 0.6666 (mtt) cc_final: 0.6413 (mtt) REVERT: A 3176 TYR cc_start: 0.7276 (t80) cc_final: 0.7063 (t80) REVERT: A 3195 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6200 (mm-30) REVERT: A 3500 MET cc_start: 0.8002 (mmm) cc_final: 0.7692 (mmm) REVERT: A 3543 PHE cc_start: 0.6844 (p90) cc_final: 0.6628 (p90) REVERT: A 3873 ARG cc_start: 0.7632 (mmt180) cc_final: 0.7364 (mmt180) REVERT: A 4075 GLU cc_start: 0.6772 (tp30) cc_final: 0.6435 (tp30) REVERT: A 4095 MET cc_start: 0.7847 (tmm) cc_final: 0.7217 (ttp) REVERT: A 4465 SER cc_start: 0.8454 (m) cc_final: 0.8160 (t) REVERT: B 101 LYS cc_start: 0.5704 (OUTLIER) cc_final: 0.5319 (mmtm) REVERT: B 311 LEU cc_start: 0.5457 (mm) cc_final: 0.5237 (mm) outliers start: 60 outliers final: 49 residues processed: 400 average time/residue: 0.6328 time to fit residues: 401.6757 Evaluate side-chains 399 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 346 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1888 CYS Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2621 ASN Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2693 TYR Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2773 MET Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2971 ASP Chi-restraints excluded: chain A residue 3021 PHE Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3675 PHE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3822 HIS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 4030 ILE Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4452 ILE Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 359 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 249 optimal weight: 0.0670 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23560 Z= 0.225 Angle : 0.575 8.480 31952 Z= 0.294 Chirality : 0.039 0.152 3590 Planarity : 0.004 0.047 4070 Dihedral : 6.647 166.009 3155 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 2.40 % Allowed : 18.17 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2810 helix: 0.99 (0.14), residues: 1409 sheet: -1.08 (0.27), residues: 354 loop : -1.09 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A4534 HIS 0.005 0.001 HIS A4187 PHE 0.016 0.001 PHE A3738 TYR 0.023 0.001 TYR A3552 ARG 0.005 0.000 ARG A2726 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 354 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1823 ARG cc_start: 0.7572 (ttp-110) cc_final: 0.7218 (tpt-90) REVERT: A 1877 ASP cc_start: 0.7746 (t0) cc_final: 0.6980 (p0) REVERT: A 1888 CYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8302 (m) REVERT: A 1960 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8330 (m-10) REVERT: A 2012 MET cc_start: 0.8861 (tmm) cc_final: 0.7814 (tmm) REVERT: A 2175 MET cc_start: 0.6615 (mtt) cc_final: 0.6355 (mtt) REVERT: A 3176 TYR cc_start: 0.7421 (t80) cc_final: 0.7165 (t80) REVERT: A 3195 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6367 (mm-30) REVERT: A 3500 MET cc_start: 0.8093 (mmm) cc_final: 0.7790 (mmm) REVERT: A 3870 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.6057 (mmt-90) REVERT: A 4075 GLU cc_start: 0.6779 (tp30) cc_final: 0.6418 (tp30) REVERT: A 4465 SER cc_start: 0.8456 (m) cc_final: 0.8178 (t) REVERT: B 101 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.5372 (mmtm) REVERT: B 311 LEU cc_start: 0.5575 (mm) cc_final: 0.5311 (mm) outliers start: 61 outliers final: 48 residues processed: 395 average time/residue: 0.6176 time to fit residues: 389.8381 Evaluate side-chains 398 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1888 CYS Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2621 ASN Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2693 TYR Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2971 ASP Chi-restraints excluded: chain A residue 3021 PHE Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3675 PHE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3814 THR Chi-restraints excluded: chain A residue 3822 HIS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3870 ARG Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4030 ILE Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4452 ILE Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 359 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 chunk 255 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 200 optimal weight: 0.0170 chunk 78 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 241 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23560 Z= 0.169 Angle : 0.548 9.322 31952 Z= 0.276 Chirality : 0.038 0.152 3590 Planarity : 0.004 0.046 4070 Dihedral : 6.377 159.981 3153 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.97 % Allowed : 18.65 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2810 helix: 1.26 (0.14), residues: 1404 sheet: -0.99 (0.27), residues: 354 loop : -0.93 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A4534 HIS 0.004 0.001 HIS A4397 PHE 0.016 0.001 PHE A3513 TYR 0.021 0.001 TYR A3552 ARG 0.005 0.000 ARG A2726 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 358 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1842 MET cc_start: 0.7591 (tpp) cc_final: 0.7315 (tpt) REVERT: A 1877 ASP cc_start: 0.7660 (t0) cc_final: 0.7002 (p0) REVERT: A 1888 CYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8247 (m) REVERT: A 1960 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8326 (m-10) REVERT: A 2012 MET cc_start: 0.8849 (tmm) cc_final: 0.7770 (tmm) REVERT: A 2175 MET cc_start: 0.6560 (mtt) cc_final: 0.6305 (mtt) REVERT: A 3176 TYR cc_start: 0.7476 (t80) cc_final: 0.7220 (t80) REVERT: A 3195 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6297 (mm-30) REVERT: A 3500 MET cc_start: 0.8183 (tmm) cc_final: 0.7889 (mmm) REVERT: A 3870 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.5978 (mmt-90) REVERT: A 4075 GLU cc_start: 0.6659 (tp30) cc_final: 0.6285 (tp30) REVERT: A 4095 MET cc_start: 0.7873 (tmm) cc_final: 0.7218 (ttp) REVERT: A 4465 SER cc_start: 0.8429 (m) cc_final: 0.8147 (t) REVERT: B 101 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5428 (mmtm) REVERT: B 311 LEU cc_start: 0.5314 (mm) cc_final: 0.5093 (mm) outliers start: 50 outliers final: 43 residues processed: 390 average time/residue: 0.6302 time to fit residues: 390.6513 Evaluate side-chains 397 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 349 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1888 CYS Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2621 ASN Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2693 TYR Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2971 ASP Chi-restraints excluded: chain A residue 3021 PHE Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3675 PHE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3814 THR Chi-restraints excluded: chain A residue 3822 HIS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3870 ARG Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4030 ILE Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4410 PHE Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 359 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 0.7980 chunk 164 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23560 Z= 0.270 Angle : 0.607 9.045 31952 Z= 0.313 Chirality : 0.040 0.179 3590 Planarity : 0.004 0.043 4070 Dihedral : 6.590 155.186 3153 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.52 % Rotamer: Outliers : 2.12 % Allowed : 18.57 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2810 helix: 0.89 (0.14), residues: 1407 sheet: -1.05 (0.27), residues: 355 loop : -1.16 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A4534 HIS 0.005 0.001 HIS A4187 PHE 0.017 0.002 PHE A3513 TYR 0.023 0.002 TYR A3552 ARG 0.004 0.000 ARG A2726 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 345 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1823 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7209 (tpt-90) REVERT: A 1877 ASP cc_start: 0.7826 (t0) cc_final: 0.7056 (p0) REVERT: A 1958 ASP cc_start: 0.7393 (p0) cc_final: 0.6489 (t0) REVERT: A 2012 MET cc_start: 0.8846 (tmm) cc_final: 0.7735 (tmm) REVERT: A 2500 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.7172 (t60) REVERT: A 3176 TYR cc_start: 0.7546 (t80) cc_final: 0.7259 (t80) REVERT: A 3195 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6519 (mm-30) REVERT: A 3500 MET cc_start: 0.8235 (tmm) cc_final: 0.7950 (mmm) REVERT: A 3870 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6050 (mmt-90) REVERT: A 4075 GLU cc_start: 0.6913 (tp30) cc_final: 0.6525 (tp30) REVERT: A 4465 SER cc_start: 0.8465 (m) cc_final: 0.8194 (t) REVERT: B 101 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5514 (mmtm) REVERT: B 311 LEU cc_start: 0.5412 (mm) cc_final: 0.5193 (mm) outliers start: 54 outliers final: 45 residues processed: 381 average time/residue: 0.6375 time to fit residues: 387.2666 Evaluate side-chains 387 residues out of total 2542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 338 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2237 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2621 ASN Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2693 TYR Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2971 ASP Chi-restraints excluded: chain A residue 3021 PHE Chi-restraints excluded: chain A residue 3130 TYR Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3675 PHE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3814 THR Chi-restraints excluded: chain A residue 3822 HIS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3870 ARG Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4030 ILE Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4410 PHE Chi-restraints excluded: chain A residue 4452 ILE Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 337 HIS Chi-restraints excluded: chain B residue 359 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 225 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 231 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2713 ASN A2954 ASN A3061 ASN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.136925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.117796 restraints weight = 169089.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.122025 restraints weight = 73337.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.124640 restraints weight = 40090.178| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23560 Z= 0.166 Angle : 0.553 9.234 31952 Z= 0.277 Chirality : 0.039 0.166 3590 Planarity : 0.004 0.054 4070 Dihedral : 6.265 150.287 3153 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.81 % Allowed : 18.92 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2810 helix: 1.31 (0.14), residues: 1405 sheet: -0.94 (0.27), residues: 355 loop : -0.96 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A4534 HIS 0.004 0.001 HIS A4397 PHE 0.016 0.001 PHE A3513 TYR 0.021 0.001 TYR A3552 ARG 0.005 0.000 ARG A2726 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7956.63 seconds wall clock time: 138 minutes 26.80 seconds (8306.80 seconds total)