Starting phenix.real_space_refine on Sat Feb 24 18:35:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyv_27783/02_2024/8dyv_27783_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyv_27783/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyv_27783/02_2024/8dyv_27783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyv_27783/02_2024/8dyv_27783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyv_27783/02_2024/8dyv_27783_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyv_27783/02_2024/8dyv_27783_neut_trim_updated.pdb" } 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 Residue "A ASP 1852": "OD1" <-> "OD2" Residue "A TYR 1872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1897": "OE1" <-> "OE2" Residue "A ASP 1937": "OD1" <-> "OD2" Residue "A GLU 2143": "OE1" <-> "OE2" Residue "A GLU 2205": "OE1" <-> "OE2" Residue "A ASP 2320": "OD1" <-> "OD2" Residue "A GLU 2578": "OE1" <-> "OE2" Residue "A ASP 2670": "OD1" <-> "OD2" Residue "A ASP 2835": "OD1" <-> "OD2" Residue "A GLU 2888": "OE1" <-> "OE2" Residue "A PHE 3021": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 3051": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 3054": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 3176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 3516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 3543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 3683": "OD1" <-> "OD2" Residue "A GLU 3779": "OE1" <-> "OE2" Residue "A PHE 3813": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 3901": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 3908": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 3957": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 4075": "OE1" <-> "OE2" Residue "A PHE 4410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 19.00, per 1000 atoms: 0.41 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 - 3.50 Amino acid : False - 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: 37.24 Conformation dependent library (CDL) restraints added in 4.8 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... running ksdssp... Secondary structure from input PDB file: 106 helices and 25 sheets defined 48.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.87 Creating SS restraints... Processing helix chain 'A' and resid 1705 through 1729 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 1735 through 1743 removed outlier: 4.808A pdb=" N THR A1740 " --> pdb=" O ASN A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1767 Processing helix chain 'A' and resid 1776 through 1797 removed outlier: 3.760A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1827 Processing helix chain 'A' and resid 1836 through 1839 No H-bonds generated for 'chain 'A' and resid 1836 through 1839' Processing helix chain 'A' and resid 1883 through 1897 Processing helix chain 'A' and resid 1912 through 1922 Processing helix chain 'A' and resid 1938 through 1951 Processing helix chain 'A' and resid 1964 through 1986 removed outlier: 3.713A pdb=" N VAL A1971 " --> pdb=" O MET A1967 " (cutoff:3.500A) Processing helix chain 'A' and resid 2030 through 2035 removed outlier: 4.304A pdb=" N LEU A2035 " --> pdb=" O ASN A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2046 through 2057 Processing helix chain 'A' and resid 2062 through 2079 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2090 through 2110 Processing helix chain 'A' and resid 2134 through 2144 Processing helix chain 'A' and resid 2151 through 2164 Proline residue: A2155 - end of helix removed outlier: 4.376A pdb=" N PHE A2158 " --> pdb=" O PRO A2155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A2164 " --> pdb=" O LEU A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2176 through 2188 Processing helix chain 'A' and resid 2201 through 2215 removed outlier: 3.711A pdb=" N GLN A2215 " --> pdb=" O TYR A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2230 through 2245 Processing helix chain 'A' and resid 2261 through 2265 Processing helix chain 'A' and resid 2279 through 2289 Processing helix chain 'A' and resid 2294 through 2296 No H-bonds generated for 'chain 'A' and resid 2294 through 2296' Processing helix chain 'A' and resid 2309 through 2315 removed outlier: 4.913A pdb=" N ASN A2314 " --> pdb=" O GLU A2310 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2357 Processing helix chain 'A' and resid 2371 through 2384 Processing helix chain 'A' and resid 2411 through 2423 Processing helix chain 'A' and resid 2433 through 2442 removed outlier: 3.894A pdb=" N PHE A2441 " --> pdb=" O LEU A2437 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2451 through 2475 Processing helix chain 'A' and resid 2483 through 2502 removed outlier: 4.191A pdb=" N ARG A2488 " --> pdb=" O GLU A2484 " (cutoff:3.500A) Processing helix chain 'A' and resid 2508 through 2521 Processing helix chain 'A' and resid 2534 through 2536 No H-bonds generated for 'chain 'A' and resid 2534 through 2536' Processing helix chain 'A' and resid 2548 through 2551 Processing helix chain 'A' and resid 2572 through 2586 Processing helix chain 'A' and resid 2601 through 2611 removed outlier: 3.598A pdb=" N ARG A2610 " --> pdb=" O PHE A2606 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2638 removed outlier: 4.229A pdb=" N LYS A2633 " --> pdb=" O LEU A2630 " (cutoff:3.500A) Processing helix chain 'A' and resid 2666 through 2668 No H-bonds generated for 'chain 'A' and resid 2666 through 2668' Processing helix chain 'A' and resid 2678 through 2689 removed outlier: 3.501A pdb=" N HIS A2689 " --> pdb=" O GLN A2685 " (cutoff:3.500A) Processing helix chain 'A' and resid 2725 through 2728 No H-bonds generated for 'chain 'A' and resid 2725 through 2728' Processing helix chain 'A' and resid 2740 through 2755 Processing helix chain 'A' and resid 2760 through 2781 removed outlier: 4.288A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU A2767 " --> pdb=" O THR A2764 " (cutoff:3.500A) Proline residue: A2768 - end of helix removed outlier: 3.778A pdb=" N ALA A2771 " --> pdb=" O PRO A2768 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A2776 " --> pdb=" O MET A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2797 through 2810 removed outlier: 3.574A pdb=" N ARG A2801 " --> pdb=" O ARG A2797 " (cutoff:3.500A) Processing helix chain 'A' and resid 2818 through 2832 Processing helix chain 'A' and resid 2840 through 2857 Processing helix chain 'A' and resid 2886 through 2903 Processing helix chain 'A' and resid 2913 through 2927 removed outlier: 3.818A pdb=" N ASP A2917 " --> pdb=" O ASN A2913 " (cutoff:3.500A) Processing helix chain 'A' and resid 2943 through 2953 Processing helix chain 'A' and resid 2969 through 2985 Processing helix chain 'A' and resid 2996 through 2998 No H-bonds generated for 'chain 'A' and resid 2996 through 2998' Processing helix chain 'A' and resid 3002 through 3014 Processing helix chain 'A' and resid 3024 through 3040 Processing helix chain 'A' and resid 3047 through 3061 Processing helix chain 'A' and resid 3072 through 3081 Processing helix chain 'A' and resid 3083 through 3086 Processing helix chain 'A' and resid 3099 through 3109 Processing helix chain 'A' and resid 3139 through 3163 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 3173 through 3213 Processing helix chain 'A' and resid 3474 through 3494 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) Processing helix chain 'A' and resid 3496 through 3501 Processing helix chain 'A' and resid 3503 through 3516 Processing helix chain 'A' and resid 3522 through 3538 Processing helix chain 'A' and resid 3549 through 3553 Processing helix chain 'A' and resid 3556 through 3565 Processing helix chain 'A' and resid 3571 through 3580 Processing helix chain 'A' and resid 3595 through 3603 Processing helix chain 'A' and resid 3619 through 3629 Processing helix chain 'A' and resid 3643 through 3649 Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3690 through 3692 No H-bonds generated for 'chain 'A' and resid 3690 through 3692' Processing helix chain 'A' and resid 3705 through 3720 Processing helix chain 'A' and resid 3722 through 3753 Processing helix chain 'A' and resid 3764 through 3800 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 3802 through 3820 removed outlier: 3.598A pdb=" N LEU A3818 " --> pdb=" O THR A3814 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LYS A3819 " --> pdb=" O MET A3815 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN A3820 " --> pdb=" O GLU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3829 through 3841 Processing helix chain 'A' and resid 3852 through 3874 removed outlier: 3.843A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3890 removed outlier: 4.936A pdb=" N ILE A3881 " --> pdb=" O GLN A3878 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE A3883 " --> pdb=" O HIS A3880 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3910 removed outlier: 4.621A pdb=" N HIS A3907 " --> pdb=" O ALA A3903 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE A3908 " --> pdb=" O GLU A3904 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU A3909 " --> pdb=" O PHE A3905 " (cutoff:3.500A) Processing helix chain 'A' and resid 3929 through 3940 removed outlier: 3.866A pdb=" N CYS A3940 " --> pdb=" O VAL A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3953 removed outlier: 4.317A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3955 through 3962 removed outlier: 3.980A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3982 through 3996 Processing helix chain 'A' and resid 3998 through 4013 removed outlier: 4.907A pdb=" N LEU A4002 " --> pdb=" O ASP A3999 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A4005 " --> pdb=" O LEU A4002 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A4012 " --> pdb=" O VAL A4009 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A4013 " --> pdb=" O SER A4010 " (cutoff:3.500A) Processing helix chain 'A' and resid 4015 through 4017 No H-bonds generated for 'chain 'A' and resid 4015 through 4017' Processing helix chain 'A' and resid 4027 through 4034 Processing helix chain 'A' and resid 4052 through 4062 Processing helix chain 'A' and resid 4074 through 4090 Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4103 through 4115 removed outlier: 4.175A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4136 through 4141 Processing helix chain 'A' and resid 4152 through 4163 removed outlier: 3.715A pdb=" N ASN A4156 " --> pdb=" O GLY A4152 " (cutoff:3.500A) Processing helix chain 'A' and resid 4166 through 4169 No H-bonds generated for 'chain 'A' and resid 4166 through 4169' Processing helix chain 'A' and resid 4174 through 4196 removed outlier: 4.615A pdb=" N LEU A4194 " --> pdb=" O GLN A4191 " (cutoff:3.500A) Processing helix chain 'A' and resid 4209 through 4226 Processing helix chain 'A' and resid 4235 through 4237 No H-bonds generated for 'chain 'A' and resid 4235 through 4237' Processing helix chain 'A' and resid 4240 through 4249 Processing helix chain 'A' and resid 4259 through 4272 Processing helix chain 'A' and resid 4275 through 4278 Processing helix chain 'A' and resid 4302 through 4310 removed outlier: 4.763A pdb=" N GLN A4307 " --> pdb=" O GLU A4303 " (cutoff:3.500A) Processing helix chain 'A' and resid 4318 through 4321 Processing helix chain 'A' and resid 4327 through 4346 removed outlier: 4.544A pdb=" N THR A4333 " --> pdb=" O ARG A4329 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A4337 " --> pdb=" O THR A4333 " (cutoff:3.500A) Processing helix chain 'A' and resid 4380 through 4388 removed outlier: 3.667A pdb=" N TRP A4387 " --> pdb=" O THR A4383 " (cutoff:3.500A) Processing helix chain 'A' and resid 4410 through 4439 Processing helix chain 'A' and resid 4446 through 4456 Processing helix chain 'A' and resid 4462 through 4464 No H-bonds generated for 'chain 'A' and resid 4462 through 4464' Processing helix chain 'A' and resid 4475 through 4497 Processing helix chain 'A' and resid 4517 through 4532 Processing helix chain 'A' and resid 4632 through 4637 removed outlier: 3.589A pdb=" N GLU A4637 " --> pdb=" O SER A4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.570A pdb=" N SER B 291 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 293 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id= B, first strand: chain 'A' and resid 1901 through 1906 Processing sheet with id= C, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.510A pdb=" N TRP A1954 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE A1930 " --> pdb=" O TRP A1954 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N CYS A1956 " --> pdb=" O PHE A1930 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A2013 " --> pdb=" O GLY A1955 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE A1957 " --> pdb=" O ALA A2013 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE A2015 " --> pdb=" O PHE A1957 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1997 through 2001 removed outlier: 4.333A pdb=" N ILE A1997 " --> pdb=" O VAL A2008 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2360 through 2363 Processing sheet with id= F, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id= G, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id= H, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id= I, first strand: chain 'A' and resid 2732 through 2735 removed outlier: 6.461A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) Processing sheet with id= J, 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= K, first strand: chain 'A' and resid 2958 through 2960 removed outlier: 5.904A pdb=" N ALA A2991 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS A3063 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET A2994 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL A3065 " --> pdb=" O MET A2994 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A3090 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE A2936 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASN A3092 " --> pdb=" O ILE A2936 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 3697 through 3700 removed outlier: 7.550A pdb=" N ILE A3677 " --> pdb=" O PRO A3587 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ILE A3589 " --> pdb=" O ILE A3677 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A3679 " --> pdb=" O ILE A3589 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id= N, first strand: chain 'A' and resid 4143 through 4147 Processing sheet with id= O, first strand: chain 'A' and resid 4539 through 4544 Processing sheet with id= P, first strand: chain 'A' and resid 4564 through 4566 Processing sheet with id= Q, first strand: chain 'A' and resid 4283 through 4286 removed outlier: 7.048A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 4604 through 4610 Processing sheet with id= S, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.716A pdb=" N ALA B 126 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL B 114 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 124 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE B 116 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL B 122 " --> pdb=" O PHE B 116 " (cutoff:3.500A) 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= T, 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: 6.105A pdb=" N ASP B 178 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N CYS B 184 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 228 through 230 removed outlier: 3.813A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 197 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 270 through 272 Processing sheet with id= W, 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: 6.413A pdb=" N ASP B 324 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N CYS B 330 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 341 through 346 removed outlier: 6.301A pdb=" N CYS B 356 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL B 344 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 354 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE B 346 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE B 352 " --> pdb=" O PHE B 346 " (cutoff:3.500A) 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) Processing sheet with id= Y, first strand: chain 'B' and resid 403 through 408 removed outlier: 3.894A pdb=" N THR B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 2997 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: 23.19 Time building geometry restraints manager: 38.22 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: 96.43 - 105.11: 481 105.11 - 113.78: 55651 113.78 - 122.46: 21330 122.46 - 131.13: 6330 131.13 - 139.81: 124 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: 1327 2.15 - 2.76: 86868 2.76 - 3.37: 135549 3.37 - 3.99: 167975 3.99 - 4.60: 261604 Nonbonded interactions: 653323 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 1.850 nonbonded pdb=" H THR A2944 " pdb=" O1B ADP A4704 " model vdw 1.656 1.850 ... (remaining 653318 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.400 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: 0.000 Extract box with map and model: 11.080 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 147.490 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.120 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.530 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 414 time to evaluate : 3.409 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: 0.8815 time to fit residues: 569.0876 Evaluate side-chains 387 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 385 time to evaluate : 3.583 ------------------------------------------------------------------------------- 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: 0.9980 chunk 215 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2752 ASN ** A2781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A2834 GLN A3792 GLN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23560 Z= 0.188 Angle : 0.549 8.197 31952 Z= 0.279 Chirality : 0.038 0.166 3590 Planarity : 0.004 0.056 4070 Dihedral : 7.955 176.502 3158 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.22 % Allowed : 14.00 % Favored : 84.78 % 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: 0.11 (0.16), residues: 2810 helix: 0.98 (0.14), residues: 1375 sheet: -0.71 (0.27), residues: 374 loop : -0.74 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2876 HIS 0.005 0.001 HIS A4100 PHE 0.015 0.001 PHE A3883 TYR 0.017 0.001 TYR A2496 ARG 0.010 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 418 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 387 time to evaluate : 3.634 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: 0.7897 (t0) cc_final: 0.7362 (p0) REVERT: A 2012 MET cc_start: 0.8487 (tmm) cc_final: 0.8055 (tmm) REVERT: A 2175 MET cc_start: 0.6043 (OUTLIER) cc_final: 0.5686 (mtt) REVERT: A 2349 LYS cc_start: 0.8820 (mttt) cc_final: 0.7853 (tptt) REVERT: A 2587 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 3126 MET cc_start: 0.8089 (mmm) cc_final: 0.7854 (mmm) REVERT: A 3195 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6075 (mm-30) REVERT: A 3906 GLN cc_start: 0.7247 (mm110) cc_final: 0.6224 (tt0) outliers start: 31 outliers final: 24 residues processed: 398 average time/residue: 0.8253 time to fit residues: 511.5307 Evaluate side-chains 389 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 363 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2175 MET 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 2621 ASN Chi-restraints excluded: chain A residue 2664 ASP Chi-restraints excluded: chain A residue 2774 VAL Chi-restraints excluded: chain A residue 2906 ASP Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3637 ASP 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 3875 MET 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 4617 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 0.0570 chunk 80 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 279 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1457 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= 0.241 Angle : 0.576 7.942 31952 Z= 0.297 Chirality : 0.038 0.157 3590 Planarity : 0.004 0.047 4070 Dihedral : 7.711 179.228 3156 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.40 % Allowed : 14.12 % Favored : 83.48 % 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: 0.72 (0.14), residues: 1379 sheet: -0.73 (0.27), residues: 367 loop : -1.02 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A4534 HIS 0.005 0.001 HIS A3880 PHE 0.016 0.002 PHE A4620 TYR 0.020 0.002 TYR A2496 ARG 0.004 0.000 ARG A2831 *********************** 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 420 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 359 time to evaluate : 3.653 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: A 1877 ASP cc_start: 0.7852 (t0) cc_final: 0.7211 (p0) REVERT: A 2012 MET cc_start: 0.8618 (tmm) cc_final: 0.8044 (tmm) REVERT: A 2349 LYS cc_start: 0.8963 (mttt) cc_final: 0.8016 (tptt) REVERT: A 3195 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6033 (mm-30) REVERT: B 381 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.7039 (t70) outliers start: 61 outliers final: 49 residues processed: 383 average time/residue: 0.8056 time to fit residues: 490.3603 Evaluate side-chains 396 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 345 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2217 ASN 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 2500 TRP Chi-restraints excluded: chain A residue 2584 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2664 ASP Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2774 VAL Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2906 ASP Chi-restraints excluded: chain A residue 2914 GLU Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2971 ASP Chi-restraints excluded: chain A residue 3089 CYS Chi-restraints excluded: chain A residue 3195 GLU Chi-restraints excluded: chain A residue 3557 ASP 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 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 3902 ASP Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4247 MET 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 4617 ASP Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 236 TRP Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 354 LEU 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: 9.9990 chunk 194 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3907 HIS A4062 GLN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4108 GLN A4191 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23560 Z= 0.368 Angle : 0.668 9.918 31952 Z= 0.356 Chirality : 0.041 0.166 3590 Planarity : 0.005 0.053 4070 Dihedral : 7.860 169.401 3156 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.05 % Favored : 92.92 % Rotamer: Outliers : 3.46 % Allowed : 15.62 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 2810 helix: -0.08 (0.13), residues: 1375 sheet: -0.93 (0.27), residues: 364 loop : -1.52 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2825 HIS 0.026 0.002 HIS B 381 PHE 0.022 0.002 PHE A4620 TYR 0.027 0.002 TYR A2496 ARG 0.005 0.001 ARG A2831 *********************** 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 438 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 350 time to evaluate : 3.910 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: A 1823 ARG cc_start: 0.7614 (ttp-110) cc_final: 0.7239 (tpt-90) REVERT: A 1877 ASP cc_start: 0.7993 (t0) cc_final: 0.7568 (p0) REVERT: A 2012 MET cc_start: 0.8788 (tmm) cc_final: 0.8137 (tmm) REVERT: A 2221 MET cc_start: 0.8365 (ttm) cc_final: 0.8045 (ttm) REVERT: A 2349 LYS cc_start: 0.9027 (mttt) cc_final: 0.8105 (tptt) REVERT: A 2500 TRP cc_start: 0.8155 (OUTLIER) cc_final: 0.7522 (t60) REVERT: A 2621 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.6814 (p0) REVERT: A 3020 LEU cc_start: 0.8633 (mt) cc_final: 0.8191 (pp) REVERT: A 3195 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6523 (mm-30) REVERT: A 4095 MET cc_start: 0.7780 (tmm) cc_final: 0.7210 (ttp) REVERT: B 101 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.5323 (mmtm) REVERT: B 383 VAL cc_start: 0.8908 (t) cc_final: 0.8625 (p) outliers start: 88 outliers final: 64 residues processed: 401 average time/residue: 0.7879 time to fit residues: 502.7036 Evaluate side-chains 411 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 343 time to evaluate : 3.661 ------------------------------------------------------------------------------- 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 1813 THR Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2217 ASN 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 2457 SER Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2621 ASN Chi-restraints excluded: chain A residue 2663 CYS 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 2803 VAL Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2840 ASP Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2880 ASP Chi-restraints excluded: chain A residue 2906 ASP Chi-restraints excluded: chain A residue 2914 GLU Chi-restraints excluded: chain A residue 2934 LEU 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 3557 ASP Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3662 ILE 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 3875 MET Chi-restraints excluded: chain A residue 3886 LEU Chi-restraints excluded: chain A residue 3902 ASP Chi-restraints excluded: chain A residue 4002 LEU 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 4175 GLU Chi-restraints excluded: chain A residue 4220 ASP 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 4465 SER Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4619 ILE 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 248 LEU Chi-restraints excluded: chain B residue 344 VAL 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: 0.5980 chunk 155 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN ** A1931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23560 Z= 0.213 Angle : 0.572 9.187 31952 Z= 0.293 Chirality : 0.039 0.154 3590 Planarity : 0.004 0.048 4070 Dihedral : 7.450 168.641 3153 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.99 % Allowed : 16.72 % Favored : 80.29 % 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: -0.74 (0.16), residues: 2810 helix: 0.35 (0.14), residues: 1381 sheet: -0.82 (0.28), residues: 361 loop : -1.39 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2500 HIS 0.006 0.001 HIS A4397 PHE 0.016 0.001 PHE A4620 TYR 0.019 0.001 TYR A2496 ARG 0.003 0.000 ARG A2831 *********************** 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 433 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 357 time to evaluate : 3.827 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: A 1823 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7202 (tpt-90) REVERT: A 1842 MET cc_start: 0.7655 (tpp) cc_final: 0.7375 (tpt) REVERT: A 1877 ASP cc_start: 0.7954 (t0) cc_final: 0.7599 (p0) REVERT: A 2012 MET cc_start: 0.8789 (tmm) cc_final: 0.8070 (tmm) REVERT: A 2221 MET cc_start: 0.8219 (ttm) cc_final: 0.8010 (ttm) REVERT: A 2621 ASN cc_start: 0.7038 (OUTLIER) cc_final: 0.6829 (p0) REVERT: A 2746 GLN cc_start: 0.8144 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 3195 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6461 (mm-30) REVERT: A 4095 MET cc_start: 0.7818 (tmm) cc_final: 0.7212 (ttp) REVERT: B 101 LYS cc_start: 0.5725 (OUTLIER) cc_final: 0.5313 (mmtm) REVERT: B 293 ILE cc_start: 0.8939 (mt) cc_final: 0.8696 (mm) outliers start: 76 outliers final: 65 residues processed: 399 average time/residue: 0.7976 time to fit residues: 504.0196 Evaluate side-chains 411 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 343 time to evaluate : 3.539 ------------------------------------------------------------------------------- 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 1813 THR Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2217 ASN 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 2457 SER 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 2681 SER 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 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 2880 ASP Chi-restraints excluded: chain A residue 2906 ASP Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2914 GLU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3021 PHE 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 3637 ASP Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3662 ILE 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 3838 ASN 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 4002 LEU Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4175 GLU Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4259 GLU 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 344 VAL Chi-restraints excluded: chain B residue 354 LEU 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: 1.9990 chunk 247 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 228 optimal weight: 0.0970 chunk 127 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 144 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: ** A1931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23560 Z= 0.265 Angle : 0.593 7.012 31952 Z= 0.308 Chirality : 0.039 0.153 3590 Planarity : 0.004 0.049 4070 Dihedral : 7.353 161.150 3153 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.90 % Favored : 93.06 % Rotamer: Outliers : 3.74 % Allowed : 16.76 % Favored : 79.50 % 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: -0.83 (0.16), residues: 2810 helix: 0.31 (0.14), residues: 1377 sheet: -0.83 (0.27), residues: 355 loop : -1.48 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2825 HIS 0.005 0.001 HIS A4397 PHE 0.017 0.002 PHE A4620 TYR 0.021 0.002 TYR A2496 ARG 0.003 0.000 ARG A4615 *********************** 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 442 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 347 time to evaluate : 3.614 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: A 1823 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.7207 (tpt-90) REVERT: A 1842 MET cc_start: 0.7716 (tpp) cc_final: 0.7421 (tpt) REVERT: A 1877 ASP cc_start: 0.7985 (t0) cc_final: 0.7668 (p0) REVERT: A 1960 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8455 (m-10) REVERT: A 2012 MET cc_start: 0.8834 (tmm) cc_final: 0.8111 (tmm) REVERT: A 2221 MET cc_start: 0.8337 (ttm) cc_final: 0.8049 (ttm) REVERT: A 2519 ARG cc_start: 0.8069 (tpt-90) cc_final: 0.7780 (tpt-90) REVERT: A 2746 GLN cc_start: 0.8174 (tt0) cc_final: 0.7780 (tm-30) REVERT: A 2953 MET cc_start: 0.7828 (ttt) cc_final: 0.7563 (ttp) REVERT: A 3195 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6737 (mm-30) REVERT: A 3500 MET cc_start: 0.7835 (mmm) cc_final: 0.7633 (mmm) REVERT: A 3543 PHE cc_start: 0.7086 (p90) cc_final: 0.6784 (p90) REVERT: A 3870 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6093 (mmt-90) REVERT: B 101 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.5351 (mmtm) REVERT: B 256 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: B 293 ILE cc_start: 0.8985 (mt) cc_final: 0.8781 (mm) outliers start: 95 outliers final: 80 residues processed: 407 average time/residue: 0.7934 time to fit residues: 511.6738 Evaluate side-chains 424 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 339 time to evaluate : 3.641 ------------------------------------------------------------------------------- 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 1813 THR Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2045 ASP Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2277 ASP Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2349 LYS 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 2457 SER Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2636 ASP 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 2774 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 2844 ARG Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2880 ASP Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2906 ASP Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2914 GLU Chi-restraints excluded: chain A residue 2934 LEU 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 3195 GLU Chi-restraints excluded: chain A residue 3519 TYR Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3640 SER Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3662 ILE 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 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 3902 ASP Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4175 GLU Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4328 GLU 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 4410 PHE Chi-restraints excluded: chain A residue 4484 GLU 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 256 GLN Chi-restraints excluded: chain B residue 344 VAL 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: 20.0000 chunk 30 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 200 optimal weight: 0.0270 chunk 155 optimal weight: 0.3980 chunk 231 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23560 Z= 0.163 Angle : 0.537 6.698 31952 Z= 0.270 Chirality : 0.038 0.152 3590 Planarity : 0.004 0.050 4070 Dihedral : 6.778 155.206 3153 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.60 % Allowed : 18.21 % Favored : 79.19 % 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: -0.23 (0.16), residues: 2810 helix: 0.84 (0.14), residues: 1374 sheet: -0.72 (0.28), residues: 350 loop : -1.20 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A4534 HIS 0.004 0.001 HIS A4397 PHE 0.013 0.001 PHE A4620 TYR 0.021 0.001 TYR A3552 ARG 0.003 0.000 ARG B 273 *********************** 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 433 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 367 time to evaluate : 3.678 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: A 1823 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.7203 (tpt-90) REVERT: A 1842 MET cc_start: 0.7600 (tpp) cc_final: 0.7330 (tpt) REVERT: A 1877 ASP cc_start: 0.7930 (t0) cc_final: 0.7637 (p0) REVERT: A 1960 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8343 (m-10) REVERT: A 2012 MET cc_start: 0.8818 (tmm) cc_final: 0.8072 (tmm) REVERT: A 2221 MET cc_start: 0.8218 (ttm) cc_final: 0.7966 (ttm) REVERT: A 2500 TRP cc_start: 0.7695 (OUTLIER) cc_final: 0.7099 (t60) REVERT: A 2746 GLN cc_start: 0.8081 (tt0) cc_final: 0.7736 (tm-30) REVERT: A 2953 MET cc_start: 0.7544 (ttt) cc_final: 0.7317 (ttp) REVERT: A 3195 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6673 (mm-30) REVERT: A 3543 PHE cc_start: 0.7025 (p90) cc_final: 0.6709 (p90) REVERT: A 4095 MET cc_start: 0.7847 (tmm) cc_final: 0.7215 (ttp) REVERT: A 4192 GLU cc_start: 0.8073 (tt0) cc_final: 0.7591 (tt0) outliers start: 66 outliers final: 54 residues processed: 409 average time/residue: 0.7928 time to fit residues: 511.2236 Evaluate side-chains 407 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 350 time to evaluate : 4.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1828 SER Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU 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 2774 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 2844 ARG Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2906 ASP Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU 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 3640 SER Chi-restraints excluded: chain A residue 3662 ILE 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 3838 ASN Chi-restraints excluded: chain A residue 3870 ARG Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4175 GLU Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4410 PHE Chi-restraints excluded: chain A residue 4484 GLU 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 344 VAL 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: 2.9990 chunk 109 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 135 optimal weight: 0.0470 chunk 25 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 249 optimal weight: 0.0000 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2380 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= 0.167 Angle : 0.537 7.032 31952 Z= 0.269 Chirality : 0.038 0.153 3590 Planarity : 0.004 0.050 4070 Dihedral : 6.511 154.206 3153 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.64 % Allowed : 18.17 % Favored : 79.19 % 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: -0.07 (0.16), residues: 2810 helix: 0.99 (0.14), residues: 1372 sheet: -0.69 (0.28), residues: 350 loop : -1.11 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4534 HIS 0.005 0.001 HIS B 337 PHE 0.013 0.001 PHE A3513 TYR 0.016 0.001 TYR A3552 ARG 0.004 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 424 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 357 time to evaluate : 3.599 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: A 1823 ARG cc_start: 0.7420 (ttp-110) cc_final: 0.7200 (tpt-90) REVERT: A 1877 ASP cc_start: 0.7935 (t0) cc_final: 0.7647 (p0) REVERT: A 1921 HIS cc_start: 0.8135 (m-70) cc_final: 0.7879 (m-70) REVERT: A 1960 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8395 (m-10) REVERT: A 2012 MET cc_start: 0.8817 (tmm) cc_final: 0.8057 (tmm) REVERT: A 2221 MET cc_start: 0.8243 (ttm) cc_final: 0.7632 (ttm) REVERT: A 2361 MET cc_start: 0.7578 (mmm) cc_final: 0.7135 (mmm) REVERT: A 2746 GLN cc_start: 0.8065 (tt0) cc_final: 0.7742 (tm-30) REVERT: A 2953 MET cc_start: 0.7638 (ttt) cc_final: 0.7436 (ttt) REVERT: A 3176 TYR cc_start: 0.7186 (t80) cc_final: 0.6967 (t80) REVERT: A 3195 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6745 (mm-30) REVERT: A 3543 PHE cc_start: 0.7085 (p90) cc_final: 0.6847 (p90) REVERT: A 4095 MET cc_start: 0.7848 (tmm) cc_final: 0.7214 (ttp) REVERT: A 4192 GLU cc_start: 0.8038 (tt0) cc_final: 0.7581 (tt0) REVERT: B 293 ILE cc_start: 0.8909 (mt) cc_final: 0.8619 (mm) outliers start: 67 outliers final: 59 residues processed: 400 average time/residue: 0.7855 time to fit residues: 496.9882 Evaluate side-chains 411 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 350 time to evaluate : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2593 LEU 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 2713 ASN Chi-restraints excluded: chain A residue 2774 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 2844 ARG Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2906 ASP Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2934 LEU 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 3640 SER Chi-restraints excluded: chain A residue 3662 ILE 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 3838 ASN Chi-restraints excluded: chain A residue 3870 ARG Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4175 GLU Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4328 GLU Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4410 PHE Chi-restraints excluded: chain A residue 4484 GLU 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 325 VAL Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 200 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 230 optimal weight: 7.9990 chunk 241 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2329 ASN ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23560 Z= 0.161 Angle : 0.530 8.699 31952 Z= 0.265 Chirality : 0.038 0.151 3590 Planarity : 0.004 0.074 4070 Dihedral : 6.295 160.733 3153 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.48 % Allowed : 18.41 % Favored : 79.11 % 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: 1.14 (0.14), residues: 1373 sheet: -0.65 (0.28), residues: 358 loop : -1.03 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4534 HIS 0.003 0.001 HIS A4397 PHE 0.015 0.001 PHE A3513 TYR 0.016 0.001 TYR A3552 ARG 0.009 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 421 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 358 time to evaluate : 3.842 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 1877 ASP cc_start: 0.7935 (t0) cc_final: 0.7671 (p0) REVERT: A 1921 HIS cc_start: 0.8130 (m-70) cc_final: 0.7887 (m-70) REVERT: A 1960 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8363 (m-10) REVERT: A 2012 MET cc_start: 0.8830 (tmm) cc_final: 0.8037 (tmm) REVERT: A 2175 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5730 (mtt) REVERT: A 2221 MET cc_start: 0.8210 (ttm) cc_final: 0.7963 (ttm) REVERT: A 2746 GLN cc_start: 0.8010 (tt0) cc_final: 0.7714 (tm-30) REVERT: A 2953 MET cc_start: 0.7627 (ttt) cc_final: 0.7413 (ttt) REVERT: A 3176 TYR cc_start: 0.7311 (t80) cc_final: 0.7108 (t80) REVERT: A 3195 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: A 3543 PHE cc_start: 0.7010 (p90) cc_final: 0.6764 (p90) REVERT: A 4192 GLU cc_start: 0.8058 (tt0) cc_final: 0.7637 (tt0) REVERT: B 101 LYS cc_start: 0.5667 (OUTLIER) cc_final: 0.5270 (mmtm) REVERT: B 293 ILE cc_start: 0.8930 (mt) cc_final: 0.8648 (mm) outliers start: 63 outliers final: 54 residues processed: 397 average time/residue: 0.8293 time to fit residues: 520.1941 Evaluate side-chains 411 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 353 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2457 SER 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 2693 TYR Chi-restraints excluded: chain A residue 2713 ASN Chi-restraints excluded: chain A residue 2774 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 2844 ARG Chi-restraints excluded: chain A residue 2874 SER Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2906 ASP Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2934 LEU 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 3640 SER Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3675 PHE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3822 HIS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3838 ASN Chi-restraints excluded: chain A residue 3870 ARG Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4175 GLU Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4328 GLU Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4410 PHE Chi-restraints excluded: chain A residue 4484 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 0.4980 chunk 187 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 178 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN ** A1931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23560 Z= 0.302 Angle : 0.625 7.701 31952 Z= 0.327 Chirality : 0.040 0.180 3590 Planarity : 0.005 0.070 4070 Dihedral : 6.620 169.971 3153 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.51 % Favored : 92.46 % Rotamer: Outliers : 2.75 % Allowed : 18.29 % Favored : 78.95 % 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: -0.71 (0.16), residues: 2810 helix: 0.42 (0.14), residues: 1367 sheet: -0.86 (0.27), residues: 358 loop : -1.40 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A4534 HIS 0.007 0.001 HIS A2918 PHE 0.018 0.002 PHE A3513 TYR 0.024 0.002 TYR A2496 ARG 0.008 0.001 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 405 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 335 time to evaluate : 3.792 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: A 1823 ARG cc_start: 0.7440 (ttp-110) cc_final: 0.7198 (tpt-90) REVERT: A 1877 ASP cc_start: 0.7975 (t0) cc_final: 0.7723 (p0) REVERT: A 1921 HIS cc_start: 0.8295 (m-70) cc_final: 0.8066 (m-70) REVERT: A 1960 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8470 (m-10) REVERT: A 2012 MET cc_start: 0.8933 (tmm) cc_final: 0.8211 (tmm) REVERT: A 2221 MET cc_start: 0.8353 (ttm) cc_final: 0.7720 (ttm) REVERT: A 2361 MET cc_start: 0.7428 (mmm) cc_final: 0.6946 (mmm) REVERT: A 2500 TRP cc_start: 0.8142 (OUTLIER) cc_final: 0.7235 (t60) REVERT: A 2746 GLN cc_start: 0.8208 (tt0) cc_final: 0.7869 (tm-30) REVERT: A 3195 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6940 (mm-30) REVERT: A 3500 MET cc_start: 0.7796 (mmm) cc_final: 0.7253 (mmm) REVERT: A 3543 PHE cc_start: 0.7235 (p90) cc_final: 0.6980 (p90) REVERT: A 4192 GLU cc_start: 0.8145 (tt0) cc_final: 0.7740 (tt0) REVERT: B 101 LYS cc_start: 0.5838 (OUTLIER) cc_final: 0.5401 (mmtm) REVERT: B 234 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8128 (ttp80) REVERT: B 293 ILE cc_start: 0.8972 (mt) cc_final: 0.8769 (mm) outliers start: 70 outliers final: 61 residues processed: 381 average time/residue: 0.8071 time to fit residues: 483.4751 Evaluate side-chains 395 residues out of total 2542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 330 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1813 THR Chi-restraints excluded: chain A residue 1828 SER Chi-restraints excluded: chain A residue 1859 ILE Chi-restraints excluded: chain A residue 1882 THR Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2217 ASN Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2500 TRP Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2621 ASN 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 2713 ASN Chi-restraints excluded: chain A residue 2774 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 2885 ASP Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2906 ASP Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2934 LEU 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 3640 SER Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3675 PHE Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 3822 HIS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3838 ASN Chi-restraints excluded: chain A residue 3870 ARG Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 3902 ASP Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4124 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4175 GLU Chi-restraints excluded: chain A residue 4220 ASP Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4314 ASP Chi-restraints excluded: chain A residue 4328 GLU Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4410 PHE Chi-restraints excluded: chain A residue 4484 GLU 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 325 VAL Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.0670 chunk 198 optimal weight: 0.0570 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN ** A3843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.134738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.116069 restraints weight = 172016.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.120136 restraints weight = 74906.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.122622 restraints weight = 41309.333| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2708 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= 0.196 Angle : 0.563 8.229 31952 Z= 0.285 Chirality : 0.038 0.151 3590 Planarity : 0.004 0.072 4070 Dihedral : 6.507 175.480 3153 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.56 % Allowed : 18.73 % Favored : 78.72 % 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: -0.38 (0.16), residues: 2810 helix: 0.73 (0.14), residues: 1372 sheet: -0.76 (0.27), residues: 358 loop : -1.29 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4534 HIS 0.005 0.001 HIS A4397 PHE 0.017 0.001 PHE A3513 TYR 0.018 0.001 TYR A2496 ARG 0.009 0.000 ARG A2726 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10101.23 seconds wall clock time: 180 minutes 33.84 seconds (10833.84 seconds total)