Starting phenix.real_space_refine on Fri Sep 19 03:41:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0y_47377/09_2025/9e0y_47377.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0y_47377/09_2025/9e0y_47377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e0y_47377/09_2025/9e0y_47377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0y_47377/09_2025/9e0y_47377.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e0y_47377/09_2025/9e0y_47377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0y_47377/09_2025/9e0y_47377.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 112 5.16 5 C 14080 2.51 5 N 3838 2.21 5 O 4161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22201 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 22085 Classifications: {'peptide': 2753} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 124, 'TRANS': 2625} Chain breaks: 3 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'ADP': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.62, per 1000 atoms: 0.21 Number of scatterers: 22201 At special positions: 0 Unit cell: (103.785, 167.365, 149.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 10 15.00 O 4161 8.00 N 3838 7.00 C 14080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5228 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 16 sheets defined 59.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 1621 through 1626 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1651 Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.834A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1775 through 1796 Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.606A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1924 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 4.273A pdb=" N GLY A1942 " --> pdb=" O PHE A1938 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.650A pdb=" N ARG A1962 " --> pdb=" O GLU A1959 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1959 through 1963' Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 2029 through 2033 removed outlier: 3.854A pdb=" N LYS A2033 " --> pdb=" O ASP A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 removed outlier: 4.072A pdb=" N LEU A2065 " --> pdb=" O THR A2061 " (cutoff:3.500A) Proline residue: A2071 - end of helix removed outlier: 3.903A pdb=" N LYS A2074 " --> pdb=" O VAL A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 removed outlier: 3.618A pdb=" N ASN A2130 " --> pdb=" O GLU A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2312 through 2320 removed outlier: 4.268A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2359 removed outlier: 3.801A pdb=" N CYS A2359 " --> pdb=" O THR A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2369 removed outlier: 3.809A pdb=" N LEU A2369 " --> pdb=" O GLU A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2384 Processing helix chain 'A' and resid 2390 through 2396 removed outlier: 3.766A pdb=" N GLN A2395 " --> pdb=" O GLU A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2397 through 2399 No H-bonds generated for 'chain 'A' and resid 2397 through 2399' Processing helix chain 'A' and resid 2410 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.868A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.604A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 Processing helix chain 'A' and resid 2504 through 2506 No H-bonds generated for 'chain 'A' and resid 2504 through 2506' Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2551 No H-bonds generated for 'chain 'A' and resid 2549 through 2551' Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.944A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.816A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2638 Processing helix chain 'A' and resid 2677 through 2689 removed outlier: 3.548A pdb=" N ILE A2683 " --> pdb=" O VAL A2679 " (cutoff:3.500A) Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2759 No H-bonds generated for 'chain 'A' and resid 2757 through 2759' Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.531A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2857 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2901 Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.642A pdb=" N ASP A2917 " --> pdb=" O ASN A2913 " (cutoff:3.500A) Processing helix chain 'A' and resid 2945 through 2954 Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.950A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3004 through 3015 removed outlier: 4.239A pdb=" N MET A3008 " --> pdb=" O PHE A3004 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A3009 " --> pdb=" O LEU A3005 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.658A pdb=" N ALA A3027 " --> pdb=" O GLY A3023 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3082 through 3089 Processing helix chain 'A' and resid 3098 through 3111 removed outlier: 4.063A pdb=" N PHE A3109 " --> pdb=" O VAL A3105 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A3110 " --> pdb=" O GLY A3106 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A3111 " --> pdb=" O LYS A3107 " (cutoff:3.500A) Processing helix chain 'A' and resid 3138 through 3165 removed outlier: 3.574A pdb=" N HIS A3151 " --> pdb=" O CYS A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3210 Processing helix chain 'A' and resid 3213 through 3220 Processing helix chain 'A' and resid 3474 through 3502 removed outlier: 4.199A pdb=" N GLU A3494 " --> pdb=" O GLU A3490 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A3495 " --> pdb=" O LYS A3491 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A3496 " --> pdb=" O THR A3492 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3516 removed outlier: 4.432A pdb=" N ASP A3506 " --> pdb=" O THR A3502 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3580 Processing helix chain 'A' and resid 3595 through 3604 removed outlier: 3.606A pdb=" N PHE A3599 " --> pdb=" O GLN A3595 " (cutoff:3.500A) Processing helix chain 'A' and resid 3621 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 3.877A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3717 Processing helix chain 'A' and resid 3721 through 3732 Processing helix chain 'A' and resid 3735 through 3750 removed outlier: 4.607A pdb=" N LEU A3745 " --> pdb=" O ARG A3741 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N SER A3748 " --> pdb=" O GLN A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3765 through 3786 removed outlier: 3.563A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A3773 " --> pdb=" O THR A3769 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU A3776 " --> pdb=" O ASN A3772 " (cutoff:3.500A) Processing helix chain 'A' and resid 3788 through 3817 removed outlier: 3.729A pdb=" N GLN A3800 " --> pdb=" O THR A3796 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3818 through 3821 Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3873 Processing helix chain 'A' and resid 3876 through 3895 removed outlier: 4.331A pdb=" N ILE A3881 " --> pdb=" O HIS A3877 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR A3882 " --> pdb=" O GLN A3878 " (cutoff:3.500A) Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3941 through 3945 removed outlier: 4.194A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 4.147A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.788A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.111A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4114 Processing helix chain 'A' and resid 4135 through 4141 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 removed outlier: 3.560A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4195 removed outlier: 3.912A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.894A pdb=" N PHE A4278 " --> pdb=" O THR A4275 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP A4279 " --> pdb=" O ARG A4276 " (cutoff:3.500A) Processing helix chain 'A' and resid 4289 through 4291 No H-bonds generated for 'chain 'A' and resid 4289 through 4291' Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 removed outlier: 4.253A pdb=" N LEU A4321 " --> pdb=" O THR A4317 " (cutoff:3.500A) Processing helix chain 'A' and resid 4326 through 4345 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4403 through 4406 removed outlier: 3.607A pdb=" N LYS A4406 " --> pdb=" O GLU A4403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4403 through 4406' Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4461 through 4465 removed outlier: 3.993A pdb=" N SER A4465 " --> pdb=" O ARG A4462 " (cutoff:3.500A) Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4502 through 4507 removed outlier: 3.864A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4631 through 4639 removed outlier: 3.646A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1661 through 1665 removed outlier: 3.717A pdb=" N VAL A1690 " --> pdb=" O VAL A1673 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 12.501A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 12.342A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1845 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 3.558A pdb=" N LEU A2039 " --> pdb=" O SER A1903 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1926 through 1927 removed outlier: 6.384A pdb=" N PHE A1926 " --> pdb=" O TRP A1954 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS A1956 " --> pdb=" O PHE A1926 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ALA A1953 " --> pdb=" O ALA A2013 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE A2015 " --> pdb=" O ALA A1953 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 2249 through 2253 removed outlier: 6.175A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP A2304 " --> pdb=" O HIS A2252 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2267 through 2268 removed outlier: 3.941A pdb=" N THR A2267 " --> pdb=" O THR A2276 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A2276 " --> pdb=" O THR A2267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AA8, first strand: chain 'A' and resid 2615 through 2618 removed outlier: 3.536A pdb=" N VAL A2618 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2639 through 2644 Processing sheet with id=AB1, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.309A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3588 through 3590 removed outlier: 6.786A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 4041 through 4042 removed outlier: 5.885A pdb=" N ARG A4143 " --> pdb=" O LEU A4042 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 4069 through 4070 removed outlier: 7.156A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 5.815A pdb=" N CYS A4286 " --> pdb=" O ILE A4294 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE A4294 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 4509 through 4510 Processing sheet with id=AB7, first strand: chain 'A' and resid 4564 through 4570 removed outlier: 9.729A pdb=" N LEU A4565 " --> pdb=" O ALA A4580 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ALA A4580 " --> pdb=" O LEU A4565 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY A4567 " --> pdb=" O SER A4578 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER A4578 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3405 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: 4.60 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7341 1.34 - 1.46: 5021 1.46 - 1.58: 10117 1.58 - 1.70: 12 1.70 - 1.82: 187 Bond restraints: 22678 Sorted by residual: bond pdb=" C ARG A2811 " pdb=" N PRO A2812 " ideal model delta sigma weight residual 1.334 1.366 -0.032 8.40e-03 1.42e+04 1.46e+01 bond pdb=" CG1 ILE A3811 " pdb=" CD1 ILE A3811 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.42e+00 bond pdb=" CB MET A4004 " pdb=" CG MET A4004 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.66e+00 bond pdb=" CG1 ILE A3835 " pdb=" CD1 ILE A3835 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.50e+00 bond pdb=" CA ASN A2987 " pdb=" CB ASN A2987 " ideal model delta sigma weight residual 1.527 1.552 -0.025 1.61e-02 3.86e+03 2.44e+00 ... (remaining 22673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 30447 3.02 - 6.03: 273 6.03 - 9.05: 43 9.05 - 12.06: 0 12.06 - 15.08: 1 Bond angle restraints: 30764 Sorted by residual: angle pdb=" CB MET A4004 " pdb=" CG MET A4004 " pdb=" SD MET A4004 " ideal model delta sigma weight residual 112.70 97.62 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C LYS A2943 " pdb=" N THR A2944 " pdb=" CA THR A2944 " ideal model delta sigma weight residual 122.61 129.25 -6.64 1.56e+00 4.11e-01 1.81e+01 angle pdb=" C ASP A1933 " pdb=" N GLU A1934 " pdb=" CA GLU A1934 " ideal model delta sigma weight residual 122.08 127.74 -5.66 1.47e+00 4.63e-01 1.48e+01 angle pdb=" C LYS A2986 " pdb=" N ASN A2987 " pdb=" CA ASN A2987 " ideal model delta sigma weight residual 122.82 128.07 -5.25 1.42e+00 4.96e-01 1.37e+01 angle pdb=" C GLN A3636 " pdb=" N ASP A3637 " pdb=" CA ASP A3637 " ideal model delta sigma weight residual 122.82 127.64 -4.82 1.42e+00 4.96e-01 1.15e+01 ... (remaining 30759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12052 17.92 - 35.84: 1377 35.84 - 53.76: 255 53.76 - 71.68: 67 71.68 - 89.60: 31 Dihedral angle restraints: 13782 sinusoidal: 5731 harmonic: 8051 Sorted by residual: dihedral pdb=" CA PRO A2628 " pdb=" C PRO A2628 " pdb=" N GLU A2629 " pdb=" CA GLU A2629 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA PHE A1629 " pdb=" C PHE A1629 " pdb=" N TYR A1630 " pdb=" CA TYR A1630 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA THR A3211 " pdb=" C THR A3211 " pdb=" N VAL A3212 " pdb=" CA VAL A3212 " ideal model delta harmonic sigma weight residual 180.00 -154.03 -25.97 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 13779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2520 0.049 - 0.097: 733 0.097 - 0.146: 177 0.146 - 0.195: 18 0.195 - 0.243: 4 Chirality restraints: 3452 Sorted by residual: chirality pdb=" CB VAL A4516 " pdb=" CA VAL A4516 " pdb=" CG1 VAL A4516 " pdb=" CG2 VAL A4516 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA PRO A2628 " pdb=" N PRO A2628 " pdb=" C PRO A2628 " pdb=" CB PRO A2628 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE A3590 " pdb=" CA ILE A3590 " pdb=" CG1 ILE A3590 " pdb=" CG2 ILE A3590 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 3449 not shown) Planarity restraints: 3953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A2627 " 0.062 5.00e-02 4.00e+02 9.46e-02 1.43e+01 pdb=" N PRO A2628 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A2628 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A2628 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A2678 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C ARG A2678 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG A2678 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL A2679 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A3151 " 0.020 2.00e-02 2.50e+03 2.15e-02 6.91e+00 pdb=" CG HIS A3151 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A3151 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS A3151 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A3151 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A3151 " 0.009 2.00e-02 2.50e+03 ... (remaining 3950 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 9968 2.98 - 3.46: 24733 3.46 - 3.94: 37489 3.94 - 4.42: 41421 4.42 - 4.90: 66222 Nonbonded interactions: 179833 Sorted by model distance: nonbonded pdb=" O4' ATP A4702 " pdb=" O5' ATP A4702 " model vdw 2.502 2.432 nonbonded pdb=" O2' ADP A4704 " pdb=" O3' ADP A4704 " model vdw 2.503 2.432 nonbonded pdb=" O2' ADP A4701 " pdb=" O3' ADP A4701 " model vdw 2.512 2.432 nonbonded pdb=" N THR A3704 " pdb=" O THR A3704 " model vdw 2.584 2.496 nonbonded pdb=" C3' ADP A4704 " pdb=" O5' ADP A4704 " model vdw 2.587 2.776 ... (remaining 179828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.200 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 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 : 0.004 0.072 22678 Z= 0.183 Angle : 0.764 15.080 30764 Z= 0.393 Chirality : 0.048 0.243 3452 Planarity : 0.006 0.095 3953 Dihedral : 16.016 89.598 8554 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.15), residues: 2745 helix: -0.00 (0.13), residues: 1483 sheet: -1.92 (0.40), residues: 174 loop : -1.21 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A4140 TYR 0.024 0.002 TYR A3176 PHE 0.036 0.002 PHE A4268 TRP 0.020 0.002 TRP A1701 HIS 0.023 0.001 HIS A3151 Details of bonding type rmsd covalent geometry : bond 0.00395 (22678) covalent geometry : angle 0.76422 (30764) hydrogen bonds : bond 0.08492 ( 1152) hydrogen bonds : angle 5.84178 ( 3405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1729 LYS cc_start: 0.8888 (mttt) cc_final: 0.8647 (ptmm) REVERT: A 1861 MET cc_start: 0.6923 (mmp) cc_final: 0.6479 (mmp) REVERT: A 2012 MET cc_start: 0.8132 (ppp) cc_final: 0.7638 (ppp) REVERT: A 2188 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7537 (tm-30) REVERT: A 2792 TYR cc_start: 0.6807 (m-10) cc_final: 0.6528 (m-80) REVERT: A 2867 MET cc_start: 0.6004 (pmm) cc_final: 0.4710 (ttm) REVERT: A 3149 PHE cc_start: 0.7060 (t80) cc_final: 0.6698 (t80) REVERT: A 4020 ILE cc_start: 0.6116 (tp) cc_final: 0.5646 (tt) REVERT: A 4095 MET cc_start: 0.7007 (tmm) cc_final: 0.6712 (tmm) REVERT: A 4377 MET cc_start: 0.7255 (mmp) cc_final: 0.6467 (tmm) REVERT: A 4564 LYS cc_start: 0.8001 (ptmt) cc_final: 0.7763 (pttm) REVERT: A 4629 LYS cc_start: 0.8394 (tmmt) cc_final: 0.8076 (tptt) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.1339 time to fit residues: 60.3558 Evaluate side-chains 212 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1695 HIS A1863 ASN A1922 GLN A2252 HIS A2439 HIS A2442 GLN ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN ** A3540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3650 ASN ** A3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.139802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.112587 restraints weight = 71138.087| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 5.64 r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22678 Z= 0.145 Angle : 0.615 8.387 30764 Z= 0.310 Chirality : 0.042 0.183 3452 Planarity : 0.005 0.070 3953 Dihedral : 7.422 80.189 3085 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.27 % Allowed : 11.27 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.16), residues: 2745 helix: 0.57 (0.13), residues: 1492 sheet: -1.83 (0.42), residues: 162 loop : -1.18 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2610 TYR 0.021 0.002 TYR A3812 PHE 0.027 0.002 PHE A4613 TRP 0.019 0.001 TRP A2825 HIS 0.010 0.001 HIS A2932 Details of bonding type rmsd covalent geometry : bond 0.00324 (22678) covalent geometry : angle 0.61547 (30764) hydrogen bonds : bond 0.03962 ( 1152) hydrogen bonds : angle 5.08244 ( 3405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.840 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: A 1861 MET cc_start: 0.7197 (mmp) cc_final: 0.6899 (mmp) REVERT: A 1967 MET cc_start: 0.8421 (ppp) cc_final: 0.8220 (ppp) REVERT: A 2012 MET cc_start: 0.8144 (ppp) cc_final: 0.7725 (ppp) REVERT: A 2603 MET cc_start: 0.5402 (ttm) cc_final: 0.5126 (ttm) REVERT: A 2729 ARG cc_start: 0.7603 (tmt170) cc_final: 0.7390 (ptm-80) REVERT: A 2932 HIS cc_start: 0.6520 (t70) cc_final: 0.5788 (t-90) REVERT: A 3038 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: A 3149 PHE cc_start: 0.6983 (t80) cc_final: 0.6608 (t80) REVERT: A 3713 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7608 (mm) REVERT: A 4020 ILE cc_start: 0.6231 (tp) cc_final: 0.6011 (tt) REVERT: A 4095 MET cc_start: 0.7220 (tmm) cc_final: 0.6861 (tmm) REVERT: A 4291 HIS cc_start: 0.8443 (p-80) cc_final: 0.8237 (p-80) REVERT: A 4377 MET cc_start: 0.7254 (mmp) cc_final: 0.6531 (tmm) REVERT: A 4564 LYS cc_start: 0.7997 (ptmt) cc_final: 0.7759 (ptpp) REVERT: A 4629 LYS cc_start: 0.8438 (tmmt) cc_final: 0.8105 (tptp) outliers start: 31 outliers final: 22 residues processed: 256 average time/residue: 0.1368 time to fit residues: 56.7780 Evaluate side-chains 239 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2636 ASP Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2891 ASP Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3108 GLU Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3573 CYS Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3713 LEU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3908 PHE Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4126 LEU Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4180 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 205 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 203 optimal weight: 0.0870 chunk 255 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 267 optimal weight: 0.1980 chunk 240 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 219 optimal weight: 0.0770 chunk 149 optimal weight: 4.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.142252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.115120 restraints weight = 71549.255| |-----------------------------------------------------------------------------| r_work (start): 0.4516 rms_B_bonded: 5.88 r_work (final): 0.4516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22678 Z= 0.107 Angle : 0.572 11.138 30764 Z= 0.283 Chirality : 0.040 0.203 3452 Planarity : 0.004 0.057 3953 Dihedral : 6.960 84.946 3085 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.72 % Allowed : 13.28 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.16), residues: 2745 helix: 0.92 (0.14), residues: 1493 sheet: -1.66 (0.40), residues: 175 loop : -1.05 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1887 TYR 0.021 0.001 TYR A2496 PHE 0.027 0.001 PHE A4613 TRP 0.016 0.001 TRP A1701 HIS 0.008 0.001 HIS A2932 Details of bonding type rmsd covalent geometry : bond 0.00221 (22678) covalent geometry : angle 0.57200 (30764) hydrogen bonds : bond 0.03619 ( 1152) hydrogen bonds : angle 4.80765 ( 3405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 0.747 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: A 1861 MET cc_start: 0.7060 (mmp) cc_final: 0.6703 (mmp) REVERT: A 1892 MET cc_start: 0.7633 (mtt) cc_final: 0.7363 (mtt) REVERT: A 1967 MET cc_start: 0.8303 (ppp) cc_final: 0.8071 (ppp) REVERT: A 2012 MET cc_start: 0.8023 (ppp) cc_final: 0.7610 (ppp) REVERT: A 2461 MET cc_start: 0.6146 (mtp) cc_final: 0.5757 (mtp) REVERT: A 2603 MET cc_start: 0.5312 (ttm) cc_final: 0.4278 (tmm) REVERT: A 2678 ARG cc_start: 0.5406 (mmt180) cc_final: 0.5174 (mmt180) REVERT: A 2726 ARG cc_start: 0.5340 (tpm170) cc_final: 0.4968 (tpt170) REVERT: A 3149 PHE cc_start: 0.6966 (t80) cc_final: 0.6617 (t80) REVERT: A 3650 ASN cc_start: 0.2945 (OUTLIER) cc_final: 0.2606 (m110) REVERT: A 3791 MET cc_start: 0.6014 (mmm) cc_final: 0.5758 (mmt) REVERT: A 4109 LEU cc_start: 0.8608 (tp) cc_final: 0.8099 (pp) REVERT: A 4377 MET cc_start: 0.7243 (mmp) cc_final: 0.6489 (tmm) REVERT: A 4564 LYS cc_start: 0.7860 (ptmt) cc_final: 0.7632 (ptpp) REVERT: A 4615 ARG cc_start: 0.2134 (mtt180) cc_final: 0.1094 (mtp180) REVERT: A 4629 LYS cc_start: 0.8422 (tmmt) cc_final: 0.8128 (tptp) outliers start: 42 outliers final: 22 residues processed: 267 average time/residue: 0.1345 time to fit residues: 58.4114 Evaluate side-chains 236 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2222 MET Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2636 ASP Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3573 CYS Chi-restraints excluded: chain A residue 3650 ASN Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3715 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3908 PHE Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4126 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4180 TYR Chi-restraints excluded: chain A residue 4474 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 238 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 136 optimal weight: 0.4980 chunk 98 optimal weight: 0.0770 chunk 200 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 chunk 252 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.9078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN ** A3540 ASN ** 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 = 0.5000 r_free = 0.5000 target = 0.141810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.114731 restraints weight = 71514.232| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 5.79 r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22678 Z= 0.109 Angle : 0.577 11.580 30764 Z= 0.283 Chirality : 0.041 0.212 3452 Planarity : 0.004 0.052 3953 Dihedral : 6.772 84.782 3085 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.68 % Allowed : 15.16 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 2745 helix: 1.15 (0.14), residues: 1479 sheet: -1.54 (0.41), residues: 175 loop : -1.02 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2729 TYR 0.020 0.001 TYR A2496 PHE 0.031 0.001 PHE A4613 TRP 0.016 0.001 TRP A1701 HIS 0.008 0.001 HIS A2932 Details of bonding type rmsd covalent geometry : bond 0.00240 (22678) covalent geometry : angle 0.57692 (30764) hydrogen bonds : bond 0.03523 ( 1152) hydrogen bonds : angle 4.68550 ( 3405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1861 MET cc_start: 0.7114 (mmp) cc_final: 0.6779 (mmp) REVERT: A 1892 MET cc_start: 0.7719 (mtt) cc_final: 0.7486 (mtt) REVERT: A 1930 PHE cc_start: 0.6028 (m-80) cc_final: 0.5668 (m-80) REVERT: A 2012 MET cc_start: 0.8016 (ppp) cc_final: 0.7595 (ppp) REVERT: A 2678 ARG cc_start: 0.5504 (mmt180) cc_final: 0.5184 (mmt180) REVERT: A 2729 ARG cc_start: 0.7310 (tmt170) cc_final: 0.7003 (ttp80) REVERT: A 2932 HIS cc_start: 0.6614 (t-90) cc_final: 0.6005 (t-90) REVERT: A 3149 PHE cc_start: 0.6929 (t80) cc_final: 0.6585 (t80) REVERT: A 3791 MET cc_start: 0.6331 (mmm) cc_final: 0.6066 (mmt) REVERT: A 4291 HIS cc_start: 0.8434 (p-80) cc_final: 0.8173 (p-80) REVERT: A 4377 MET cc_start: 0.7239 (mmp) cc_final: 0.6507 (tmm) REVERT: A 4434 VAL cc_start: 0.6128 (t) cc_final: 0.5817 (p) REVERT: A 4615 ARG cc_start: 0.2279 (mtt180) cc_final: 0.0939 (mtp180) REVERT: A 4629 LYS cc_start: 0.8402 (tmmt) cc_final: 0.8120 (tptp) outliers start: 41 outliers final: 30 residues processed: 261 average time/residue: 0.1345 time to fit residues: 56.9556 Evaluate side-chains 244 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2636 ASP Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2922 ILE Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3573 CYS Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3715 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3908 PHE Chi-restraints excluded: chain A residue 3987 ILE Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4126 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4180 TYR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4543 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 245 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 222 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 0.0870 chunk 112 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN A3540 ASN ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.142161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.115207 restraints weight = 70269.700| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 5.78 r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22678 Z= 0.107 Angle : 0.574 12.294 30764 Z= 0.281 Chirality : 0.041 0.271 3452 Planarity : 0.004 0.067 3953 Dihedral : 6.615 76.643 3085 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.17 % Allowed : 15.66 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.16), residues: 2745 helix: 1.22 (0.14), residues: 1480 sheet: -1.49 (0.40), residues: 175 loop : -0.96 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1623 TYR 0.022 0.001 TYR A3176 PHE 0.028 0.001 PHE A4613 TRP 0.016 0.001 TRP A1701 HIS 0.006 0.001 HIS A2932 Details of bonding type rmsd covalent geometry : bond 0.00230 (22678) covalent geometry : angle 0.57351 (30764) hydrogen bonds : bond 0.03443 ( 1152) hydrogen bonds : angle 4.64880 ( 3405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1861 MET cc_start: 0.7132 (mmp) cc_final: 0.6845 (mmp) REVERT: A 1863 ASN cc_start: 0.8484 (t0) cc_final: 0.8218 (t0) REVERT: A 2012 MET cc_start: 0.7998 (ppp) cc_final: 0.7562 (ppp) REVERT: A 2053 MET cc_start: 0.2905 (OUTLIER) cc_final: 0.2613 (mmt) REVERT: A 2461 MET cc_start: 0.6106 (mtp) cc_final: 0.5848 (mtp) REVERT: A 2867 MET cc_start: 0.6113 (pmm) cc_final: 0.4682 (ttm) REVERT: A 2932 HIS cc_start: 0.6747 (t-90) cc_final: 0.6294 (t-90) REVERT: A 3499 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: A 3650 ASN cc_start: 0.2678 (OUTLIER) cc_final: 0.2258 (m110) REVERT: A 3791 MET cc_start: 0.6516 (mmm) cc_final: 0.6254 (mmt) REVERT: A 4291 HIS cc_start: 0.8432 (p-80) cc_final: 0.8154 (p-80) REVERT: A 4377 MET cc_start: 0.7267 (mmp) cc_final: 0.6490 (tmm) REVERT: A 4434 VAL cc_start: 0.6052 (t) cc_final: 0.5764 (p) REVERT: A 4630 GLU cc_start: 0.8272 (pm20) cc_final: 0.7935 (pm20) outliers start: 53 outliers final: 30 residues processed: 277 average time/residue: 0.1328 time to fit residues: 59.7312 Evaluate side-chains 246 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2445 HIS Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2636 ASP Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2916 LEU Chi-restraints excluded: chain A residue 2922 ILE Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3502 THR Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3573 CYS Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3650 ASN Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3715 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3908 PHE Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4126 LEU Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4180 TYR Chi-restraints excluded: chain A residue 4243 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4543 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 46 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2849 ASN ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3198 GLN A3499 GLN A3527 ASN ** A3540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4249 GLN ** A4325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.135341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.110895 restraints weight = 72815.483| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 5.18 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 22678 Z= 0.242 Angle : 0.762 12.096 30764 Z= 0.384 Chirality : 0.047 0.228 3452 Planarity : 0.005 0.059 3953 Dihedral : 7.340 77.304 3085 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 2.70 % Allowed : 17.34 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.16), residues: 2745 helix: 0.50 (0.13), residues: 1484 sheet: -1.42 (0.41), residues: 164 loop : -1.23 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1623 TYR 0.028 0.003 TYR A2055 PHE 0.027 0.003 PHE A3179 TRP 0.016 0.002 TRP A2825 HIS 0.007 0.001 HIS A2932 Details of bonding type rmsd covalent geometry : bond 0.00559 (22678) covalent geometry : angle 0.76177 (30764) hydrogen bonds : bond 0.04612 ( 1152) hydrogen bonds : angle 5.15704 ( 3405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 226 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1967 MET cc_start: 0.8539 (ppp) cc_final: 0.8252 (ppp) REVERT: A 2012 MET cc_start: 0.8059 (ppp) cc_final: 0.7505 (ppp) REVERT: A 2603 MET cc_start: 0.5758 (ttm) cc_final: 0.4686 (tmm) REVERT: A 2932 HIS cc_start: 0.6814 (t-90) cc_final: 0.5933 (t-90) REVERT: A 3108 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: A 3499 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: A 3513 PHE cc_start: 0.6880 (t80) cc_final: 0.6439 (t80) REVERT: A 3650 ASN cc_start: 0.2127 (OUTLIER) cc_final: 0.1749 (m110) REVERT: A 3791 MET cc_start: 0.5970 (mmm) cc_final: 0.5626 (mmt) REVERT: A 4140 ARG cc_start: 0.5691 (OUTLIER) cc_final: 0.5149 (mmt90) REVERT: A 4196 TYR cc_start: 0.5899 (OUTLIER) cc_final: 0.5246 (m-10) REVERT: A 4291 HIS cc_start: 0.8461 (p-80) cc_final: 0.8216 (p-80) REVERT: A 4377 MET cc_start: 0.6993 (mmp) cc_final: 0.6376 (tmm) REVERT: A 4564 LYS cc_start: 0.7726 (ptpp) cc_final: 0.7437 (pttt) outliers start: 66 outliers final: 46 residues processed: 269 average time/residue: 0.1368 time to fit residues: 60.2279 Evaluate side-chains 266 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1623 ARG Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 THR Chi-restraints excluded: chain A residue 2154 ILE Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2445 HIS Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2636 ASP Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2792 TYR Chi-restraints excluded: chain A residue 2891 ASP Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2922 ILE Chi-restraints excluded: chain A residue 3108 GLU Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3502 THR Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3573 CYS Chi-restraints excluded: chain A residue 3650 ASN Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3715 GLU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3908 PHE Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4140 ARG Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4180 TYR Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4243 LEU Chi-restraints excluded: chain A residue 4246 LEU Chi-restraints excluded: chain A residue 4323 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4644 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 215 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 218 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 260 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN ** A3540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3956 GLN ** A4325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.135108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.110054 restraints weight = 71181.365| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 4.88 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22678 Z= 0.187 Angle : 0.697 12.717 30764 Z= 0.346 Chirality : 0.045 0.246 3452 Planarity : 0.005 0.056 3953 Dihedral : 7.241 79.935 3085 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.58 % Allowed : 18.40 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.16), residues: 2745 helix: 0.57 (0.13), residues: 1486 sheet: -1.60 (0.39), residues: 176 loop : -1.23 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A4615 TYR 0.027 0.002 TYR A3176 PHE 0.027 0.002 PHE A2727 TRP 0.024 0.002 TRP A4222 HIS 0.007 0.001 HIS A2932 Details of bonding type rmsd covalent geometry : bond 0.00428 (22678) covalent geometry : angle 0.69713 (30764) hydrogen bonds : bond 0.04231 ( 1152) hydrogen bonds : angle 5.04064 ( 3405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2012 MET cc_start: 0.7959 (ppp) cc_final: 0.7395 (ppp) REVERT: A 2053 MET cc_start: 0.2906 (OUTLIER) cc_final: 0.2595 (mmt) REVERT: A 2461 MET cc_start: 0.6563 (mtp) cc_final: 0.6066 (mtp) REVERT: A 2603 MET cc_start: 0.5756 (ttm) cc_final: 0.4577 (tmm) REVERT: A 2729 ARG cc_start: 0.7533 (tmt170) cc_final: 0.7098 (ttp80) REVERT: A 2867 MET cc_start: 0.6443 (pmm) cc_final: 0.4882 (ttm) REVERT: A 2932 HIS cc_start: 0.6826 (t-90) cc_final: 0.6407 (t70) REVERT: A 3108 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: A 3169 MET cc_start: 0.3206 (OUTLIER) cc_final: 0.2995 (pmm) REVERT: A 3513 PHE cc_start: 0.6910 (t80) cc_final: 0.6537 (t80) REVERT: A 3650 ASN cc_start: 0.2131 (OUTLIER) cc_final: 0.1831 (m110) REVERT: A 3695 ARG cc_start: 0.6349 (mmt180) cc_final: 0.5816 (mmt180) REVERT: A 3791 MET cc_start: 0.5949 (mmm) cc_final: 0.5604 (mmt) REVERT: A 4109 LEU cc_start: 0.8695 (tp) cc_final: 0.8136 (pp) REVERT: A 4140 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.5208 (mmt90) REVERT: A 4291 HIS cc_start: 0.8450 (p-80) cc_final: 0.8198 (p-80) REVERT: A 4377 MET cc_start: 0.7002 (mmp) cc_final: 0.6430 (tmm) outliers start: 63 outliers final: 48 residues processed: 256 average time/residue: 0.1402 time to fit residues: 58.1956 Evaluate side-chains 267 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2144 THR Chi-restraints excluded: chain A residue 2154 ILE Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2295 LEU Chi-restraints excluded: chain A residue 2445 HIS Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2636 ASP Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2792 TYR Chi-restraints excluded: chain A residue 2891 ASP Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2916 LEU Chi-restraints excluded: chain A residue 2922 ILE Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3108 GLU Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3573 CYS Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3650 ASN Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3715 GLU Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3908 PHE Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4140 ARG Chi-restraints excluded: chain A residue 4180 TYR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4243 LEU Chi-restraints excluded: chain A residue 4245 THR Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4543 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 263 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 239 optimal weight: 0.5980 chunk 218 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN ** A3540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3869 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.136738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.109190 restraints weight = 71205.765| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 5.87 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22678 Z= 0.154 Angle : 0.669 12.814 30764 Z= 0.329 Chirality : 0.043 0.228 3452 Planarity : 0.004 0.053 3953 Dihedral : 7.143 84.529 3085 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.50 % Allowed : 19.06 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2745 helix: 0.71 (0.13), residues: 1486 sheet: -1.58 (0.39), residues: 177 loop : -1.18 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4615 TYR 0.026 0.002 TYR A3176 PHE 0.029 0.002 PHE A3496 TRP 0.025 0.002 TRP A4222 HIS 0.006 0.001 HIS A2932 Details of bonding type rmsd covalent geometry : bond 0.00351 (22678) covalent geometry : angle 0.66907 (30764) hydrogen bonds : bond 0.04009 ( 1152) hydrogen bonds : angle 4.94995 ( 3405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 215 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1710 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7288 (ttm170) REVERT: A 1938 PHE cc_start: 0.7798 (t80) cc_final: 0.7426 (t80) REVERT: A 2012 MET cc_start: 0.8011 (ppp) cc_final: 0.7513 (ppp) REVERT: A 2461 MET cc_start: 0.6427 (mtp) cc_final: 0.6010 (mtp) REVERT: A 2603 MET cc_start: 0.5805 (ttm) cc_final: 0.4522 (tmm) REVERT: A 2729 ARG cc_start: 0.7610 (tmt170) cc_final: 0.7209 (ttp80) REVERT: A 2867 MET cc_start: 0.6111 (pmm) cc_final: 0.4693 (ttm) REVERT: A 2949 PHE cc_start: 0.2526 (OUTLIER) cc_final: 0.1603 (t80) REVERT: A 3108 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: A 3149 PHE cc_start: 0.6665 (t80) cc_final: 0.6392 (t80) REVERT: A 3499 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: A 3513 PHE cc_start: 0.6795 (t80) cc_final: 0.6413 (t80) REVERT: A 3695 ARG cc_start: 0.6162 (mmt180) cc_final: 0.5606 (mmt180) REVERT: A 3791 MET cc_start: 0.6588 (mmm) cc_final: 0.6314 (mmt) REVERT: A 4109 LEU cc_start: 0.8690 (tp) cc_final: 0.8117 (pp) REVERT: A 4291 HIS cc_start: 0.8489 (p-80) cc_final: 0.8228 (p-80) REVERT: A 4377 MET cc_start: 0.6976 (mmp) cc_final: 0.6351 (tmm) REVERT: A 4564 LYS cc_start: 0.7717 (ptpp) cc_final: 0.7368 (pttt) outliers start: 61 outliers final: 41 residues processed: 253 average time/residue: 0.1449 time to fit residues: 59.9020 Evaluate side-chains 254 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1791 VAL Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2154 ILE Chi-restraints excluded: chain A residue 2445 HIS Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2636 ASP Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2792 TYR Chi-restraints excluded: chain A residue 2891 ASP Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2916 LEU Chi-restraints excluded: chain A residue 2922 ILE Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2949 PHE Chi-restraints excluded: chain A residue 3108 GLU Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3573 CYS Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3715 GLU Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3908 PHE Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4180 TYR Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4243 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4543 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 162 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 264 optimal weight: 5.9990 chunk 94 optimal weight: 0.1980 chunk 144 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 268 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN ** A3540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.139107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.111967 restraints weight = 70694.183| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 5.71 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22678 Z= 0.121 Angle : 0.646 12.678 30764 Z= 0.313 Chirality : 0.043 0.254 3452 Planarity : 0.004 0.052 3953 Dihedral : 6.957 89.478 3085 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.84 % Allowed : 19.75 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2745 helix: 0.91 (0.14), residues: 1488 sheet: -1.66 (0.38), residues: 184 loop : -1.05 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4615 TYR 0.030 0.001 TYR A3176 PHE 0.025 0.001 PHE A4613 TRP 0.025 0.001 TRP A4222 HIS 0.004 0.001 HIS A2932 Details of bonding type rmsd covalent geometry : bond 0.00265 (22678) covalent geometry : angle 0.64555 (30764) hydrogen bonds : bond 0.03713 ( 1152) hydrogen bonds : angle 4.80097 ( 3405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1710 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7263 (ttm170) REVERT: A 2012 MET cc_start: 0.7913 (ppp) cc_final: 0.7318 (ppp) REVERT: A 2461 MET cc_start: 0.6157 (mtp) cc_final: 0.5769 (mtp) REVERT: A 2729 ARG cc_start: 0.7551 (tmt170) cc_final: 0.7165 (ttp80) REVERT: A 2867 MET cc_start: 0.5932 (pmm) cc_final: 0.4509 (ttm) REVERT: A 2932 HIS cc_start: 0.7025 (t-90) cc_final: 0.6751 (t-90) REVERT: A 2949 PHE cc_start: 0.2408 (OUTLIER) cc_final: 0.1544 (t80) REVERT: A 3176 TYR cc_start: 0.6099 (t80) cc_final: 0.5772 (t80) REVERT: A 3494 GLU cc_start: 0.7460 (tp30) cc_final: 0.6405 (mp0) REVERT: A 3695 ARG cc_start: 0.5702 (mmt180) cc_final: 0.5276 (mpt90) REVERT: A 3791 MET cc_start: 0.6536 (mmm) cc_final: 0.6248 (mmt) REVERT: A 4093 TRP cc_start: 0.5172 (m-90) cc_final: 0.4674 (m-90) REVERT: A 4109 LEU cc_start: 0.8646 (tp) cc_final: 0.8070 (pp) REVERT: A 4291 HIS cc_start: 0.8433 (p-80) cc_final: 0.8167 (p-80) REVERT: A 4377 MET cc_start: 0.6947 (mmp) cc_final: 0.6343 (tmm) REVERT: A 4564 LYS cc_start: 0.7636 (ptpp) cc_final: 0.7299 (pttt) REVERT: A 4615 ARG cc_start: 0.2294 (mtt180) cc_final: 0.2020 (ptp-170) outliers start: 45 outliers final: 33 residues processed: 246 average time/residue: 0.1486 time to fit residues: 59.8350 Evaluate side-chains 246 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1951 VAL Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2154 ILE Chi-restraints excluded: chain A residue 2445 HIS Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2636 ASP Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2792 TYR Chi-restraints excluded: chain A residue 2891 ASP Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2916 LEU Chi-restraints excluded: chain A residue 2922 ILE Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2949 PHE Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3715 GLU Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3908 PHE Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4134 VAL Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4180 TYR Chi-restraints excluded: chain A residue 4243 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4644 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 182 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 97 optimal weight: 0.0010 chunk 187 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 50 optimal weight: 0.0000 chunk 223 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3139 HIS ** A3540 ASN ** 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 = 0.4959 r_free = 0.4959 target = 0.139179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.112031 restraints weight = 71092.868| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 5.73 r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22678 Z= 0.123 Angle : 0.652 12.807 30764 Z= 0.315 Chirality : 0.043 0.260 3452 Planarity : 0.004 0.055 3953 Dihedral : 6.846 82.641 3085 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.64 % Allowed : 19.96 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.16), residues: 2745 helix: 1.00 (0.14), residues: 1489 sheet: -1.68 (0.37), residues: 189 loop : -1.00 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1887 TYR 0.027 0.001 TYR A3176 PHE 0.037 0.002 PHE A2727 TRP 0.022 0.001 TRP A4222 HIS 0.004 0.001 HIS A4006 Details of bonding type rmsd covalent geometry : bond 0.00275 (22678) covalent geometry : angle 0.65245 (30764) hydrogen bonds : bond 0.03643 ( 1152) hydrogen bonds : angle 4.75119 ( 3405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.913 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: A 1710 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7250 (ttm170) REVERT: A 1930 PHE cc_start: 0.6148 (m-10) cc_final: 0.5909 (m-10) REVERT: A 2070 VAL cc_start: 0.6195 (t) cc_final: 0.5905 (t) REVERT: A 2461 MET cc_start: 0.6105 (mtp) cc_final: 0.5727 (mtp) REVERT: A 2729 ARG cc_start: 0.7619 (tmt170) cc_final: 0.7248 (ttp80) REVERT: A 2867 MET cc_start: 0.5910 (pmm) cc_final: 0.4479 (ttm) REVERT: A 2949 PHE cc_start: 0.2444 (OUTLIER) cc_final: 0.1562 (t80) REVERT: A 2987 ASN cc_start: 0.8536 (p0) cc_final: 0.7839 (m-40) REVERT: A 3176 TYR cc_start: 0.6195 (t80) cc_final: 0.5941 (t80) REVERT: A 3513 PHE cc_start: 0.6622 (t80) cc_final: 0.6211 (t80) REVERT: A 3678 PHE cc_start: 0.5898 (m-10) cc_final: 0.5518 (m-10) REVERT: A 3679 LEU cc_start: 0.6738 (tt) cc_final: 0.6279 (mt) REVERT: A 3791 MET cc_start: 0.6607 (mmm) cc_final: 0.6341 (mmt) REVERT: A 4109 LEU cc_start: 0.8644 (tp) cc_final: 0.8061 (pp) REVERT: A 4291 HIS cc_start: 0.8456 (p-80) cc_final: 0.8183 (p-80) REVERT: A 4377 MET cc_start: 0.6953 (mmp) cc_final: 0.6344 (tmm) REVERT: A 4564 LYS cc_start: 0.7638 (ptpp) cc_final: 0.7295 (pttt) REVERT: A 4615 ARG cc_start: 0.2265 (mtt180) cc_final: 0.1603 (ptp-170) outliers start: 40 outliers final: 30 residues processed: 238 average time/residue: 0.1406 time to fit residues: 55.0527 Evaluate side-chains 241 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2154 ILE Chi-restraints excluded: chain A residue 2445 HIS Chi-restraints excluded: chain A residue 2490 ILE Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2636 ASP Chi-restraints excluded: chain A residue 2750 THR Chi-restraints excluded: chain A residue 2792 TYR Chi-restraints excluded: chain A residue 2891 ASP Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2916 LEU Chi-restraints excluded: chain A residue 2922 ILE Chi-restraints excluded: chain A residue 2949 PHE Chi-restraints excluded: chain A residue 3514 ILE Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3715 GLU Chi-restraints excluded: chain A residue 3815 MET Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3908 PHE Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4243 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4543 VAL Chi-restraints excluded: chain A residue 4644 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 7 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.138490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.111208 restraints weight = 70783.525| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 5.71 r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22678 Z= 0.134 Angle : 0.661 13.351 30764 Z= 0.319 Chirality : 0.043 0.270 3452 Planarity : 0.004 0.055 3953 Dihedral : 6.873 80.861 3085 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.52 % Allowed : 20.12 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.16), residues: 2745 helix: 0.99 (0.14), residues: 1486 sheet: -1.74 (0.37), residues: 187 loop : -0.99 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1887 TYR 0.024 0.001 TYR A3176 PHE 0.030 0.002 PHE A2727 TRP 0.021 0.001 TRP A4222 HIS 0.004 0.001 HIS A2932 Details of bonding type rmsd covalent geometry : bond 0.00303 (22678) covalent geometry : angle 0.66113 (30764) hydrogen bonds : bond 0.03688 ( 1152) hydrogen bonds : angle 4.75840 ( 3405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.58 seconds wall clock time: 85 minutes 21.78 seconds (5121.78 seconds total)