Starting phenix.real_space_refine on Fri Sep 19 05:12:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm2_44685/09_2025/9bm2_44685.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm2_44685/09_2025/9bm2_44685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bm2_44685/09_2025/9bm2_44685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm2_44685/09_2025/9bm2_44685.map" model { file = "/net/cci-nas-00/data/ceres_data/9bm2_44685/09_2025/9bm2_44685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm2_44685/09_2025/9bm2_44685.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 113 5.16 5 C 14635 2.51 5 N 3980 2.21 5 O 4307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 23046 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2859, 22925 Classifications: {'peptide': 2859} Link IDs: {'PTRANS': 130, 'TRANS': 2728} Chain breaks: 3 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 121 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6, 'water': 7} Link IDs: {None: 12} Time building chain proxies: 5.03, per 1000 atoms: 0.22 Number of scatterers: 23046 At special positions: 0 Unit cell: (123.136, 188.864, 163.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 113 16.00 P 9 15.00 Mg 2 11.99 O 4307 8.00 N 3980 7.00 C 14635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 908.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 17 sheets defined 63.5% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 1536 through 1554 Processing helix chain 'A' and resid 1561 through 1583 removed outlier: 3.542A pdb=" N SER A1583 " --> pdb=" O MET A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 removed outlier: 3.525A pdb=" N ASN A1593 " --> pdb=" O MET A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1625 removed outlier: 3.641A pdb=" N SER A1600 " --> pdb=" O GLY A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1648 through 1653 removed outlier: 3.957A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.564A 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 removed outlier: 3.572A pdb=" N VAL A1751 " --> pdb=" O ALA A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.860A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1828 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 1923 Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1960 through 1963 Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.700A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2145 Processing helix chain 'A' and resid 2146 through 2149 Processing helix chain 'A' and resid 2150 through 2152 No H-bonds generated for 'chain 'A' and resid 2150 through 2152' Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 removed outlier: 3.901A pdb=" N GLU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2255 through 2259 removed outlier: 3.851A pdb=" N ILE A2259 " --> pdb=" O PRO A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.518A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2308 through 2313 removed outlier: 3.627A pdb=" N GLU A2313 " --> pdb=" O PRO A2309 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2316 No H-bonds generated for 'chain 'A' and resid 2314 through 2316' Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.682A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2431 through 2441 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.583A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.649A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.767A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.831A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.278A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2757 Processing helix chain 'A' and resid 2758 through 2764 removed outlier: 6.575A pdb=" N SER A2761 " --> pdb=" O LEU A2758 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.515A pdb=" N PHE A2776 " --> pdb=" O ALA A2772 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.846A 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 2858 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2927 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 4.031A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3062 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.685A pdb=" N LYS A3076 " --> pdb=" O SER A3072 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3111 through 3113 No H-bonds generated for 'chain 'A' and resid 3111 through 3113' Processing helix chain 'A' and resid 3138 through 3164 removed outlier: 3.506A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3241 removed outlier: 3.587A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3495 removed outlier: 4.685A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A3495 " --> pdb=" O LYS A3491 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3517 removed outlier: 5.104A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.514A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.648A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 3.558A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3756 Processing helix chain 'A' and resid 3763 through 3818 removed outlier: 3.558A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A3797 " --> pdb=" O GLU A3793 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN A3800 " --> pdb=" O THR A3796 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.616A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.695A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.584A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3894 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.185A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.536A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 removed outlier: 3.555A pdb=" N GLY A4014 " --> pdb=" O SER A4010 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.626A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.009A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.857A pdb=" N MET A4107 " --> pdb=" O PRO A4103 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.520A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.383A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 removed outlier: 3.526A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4326 through 4346 removed outlier: 4.356A pdb=" N VAL A4330 " --> pdb=" O ASN A4326 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU A4331 " --> pdb=" O ALA A4327 " (cutoff:3.500A) Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.451A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4502 through 4506 Processing helix chain 'A' and resid 4512 through 4514 No H-bonds generated for 'chain 'A' and resid 4512 through 4514' Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 7.480A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1842 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1931 Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2000 Processing sheet with id=AA6, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 6.573A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP A2304 " --> pdb=" O HIS A2252 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A2254 " --> pdb=" O ASP A2304 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.327A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 6.807A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.785A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 6.096A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.226A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.313A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.419A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.515A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1374 hydrogen bonds defined for protein. 4005 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: 6.57 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7604 1.34 - 1.46: 5034 1.46 - 1.58: 10688 1.58 - 1.70: 14 1.70 - 1.82: 189 Bond restraints: 23529 Sorted by residual: bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP A4704 " pdb=" C6 ADP A4704 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 23524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 31582 2.58 - 5.15: 291 5.15 - 7.73: 27 7.73 - 10.30: 8 10.30 - 12.88: 7 Bond angle restraints: 31915 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 133.50 6.37 1.00e+00 1.00e+00 4.05e+01 angle pdb=" PA ATP A4702 " pdb=" O3A ATP A4702 " pdb=" PB ATP A4702 " ideal model delta sigma weight residual 136.83 131.11 5.72 1.00e+00 1.00e+00 3.28e+01 angle pdb=" PA ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sigma weight residual 120.50 133.38 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CA GLY A2740 " pdb=" C GLY A2740 " pdb=" O GLY A2740 " ideal model delta sigma weight residual 122.38 118.11 4.27 1.03e+00 9.43e-01 1.72e+01 angle pdb=" PA ADP A4703 " pdb=" O3A ADP A4703 " pdb=" PB ADP A4703 " ideal model delta sigma weight residual 120.50 132.78 -12.28 3.00e+00 1.11e-01 1.67e+01 ... (remaining 31910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.93: 13924 32.93 - 65.85: 319 65.85 - 98.78: 36 98.78 - 131.71: 2 131.71 - 164.64: 1 Dihedral angle restraints: 14282 sinusoidal: 5915 harmonic: 8367 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 104.63 -164.64 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual 300.00 169.71 130.29 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual 300.00 173.68 126.32 1 2.00e+01 2.50e-03 3.82e+01 ... (remaining 14279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3021 0.055 - 0.110: 505 0.110 - 0.165: 59 0.165 - 0.219: 9 0.219 - 0.274: 1 Chirality restraints: 3595 Sorted by residual: chirality pdb=" CB THR A4267 " pdb=" CA THR A4267 " pdb=" OG1 THR A4267 " pdb=" CG2 THR A4267 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE A2049 " pdb=" N ILE A2049 " pdb=" C ILE A2049 " pdb=" CB ILE A2049 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CA VAL A1880 " pdb=" N VAL A1880 " pdb=" C VAL A1880 " pdb=" CB VAL A1880 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 3592 not shown) Planarity restraints: 4090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2025 " 0.169 9.50e-02 1.11e+02 7.56e-02 3.51e+00 pdb=" NE ARG A2025 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A2025 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A2025 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A2025 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A3136 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A3137 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A3137 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A3137 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1546 " 0.013 2.00e-02 2.50e+03 1.10e-02 2.40e+00 pdb=" CG TYR A1546 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A1546 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A1546 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A1546 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A1546 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A1546 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1546 " 0.000 2.00e-02 2.50e+03 ... (remaining 4087 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 88 2.49 - 3.09: 16476 3.09 - 3.70: 36091 3.70 - 4.30: 54152 4.30 - 4.90: 88681 Nonbonded interactions: 195488 Sorted by model distance: nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 1.891 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4706 " model vdw 2.047 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4706 " model vdw 2.141 2.170 nonbonded pdb=" OH TYR A2967 " pdb=" OD2 ASP A2975 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR A2627 " pdb=" OE1 GLU A2629 " model vdw 2.215 3.040 ... (remaining 195483 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=0.00 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: 4.870 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 0.109 23529 Z= 0.230 Angle : 0.631 12.878 31915 Z= 0.352 Chirality : 0.041 0.274 3595 Planarity : 0.004 0.076 4090 Dihedral : 14.491 164.635 8848 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.16 (0.16), residues: 2851 helix: 2.12 (0.13), residues: 1633 sheet: 0.04 (0.33), residues: 252 loop : 0.78 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1966 TYR 0.027 0.001 TYR A1546 PHE 0.016 0.001 PHE A1926 TRP 0.022 0.001 TRP A1701 HIS 0.006 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00391 (23529) covalent geometry : angle 0.63065 (31915) hydrogen bonds : bond 0.12327 ( 1374) hydrogen bonds : angle 5.33920 ( 4005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 2306 ASP cc_start: 0.8573 (m-30) cc_final: 0.8357 (m-30) REVERT: A 3743 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7490 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.7706 time to fit residues: 339.0408 Evaluate side-chains 252 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.0870 chunk 111 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1695 HIS ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 ASN A2187 GLN A2482 GLN A2621 ASN A2827 HIS A3069 ASN A3906 GLN A4098 ASN A4231 GLN A4466 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115073 restraints weight = 28614.489| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.70 r_work: 0.3210 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23529 Z= 0.119 Angle : 0.497 7.672 31915 Z= 0.251 Chirality : 0.039 0.141 3595 Planarity : 0.004 0.045 4090 Dihedral : 7.246 175.414 3175 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.86 % Allowed : 7.58 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.39 (0.16), residues: 2851 helix: 2.35 (0.13), residues: 1653 sheet: -0.26 (0.32), residues: 255 loop : 0.90 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3164 TYR 0.023 0.001 TYR A1546 PHE 0.017 0.001 PHE A1575 TRP 0.017 0.001 TRP A1701 HIS 0.004 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00261 (23529) covalent geometry : angle 0.49737 (31915) hydrogen bonds : bond 0.04019 ( 1374) hydrogen bonds : angle 4.20494 ( 4005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.798 Fit side-chains REVERT: A 1950 GLN cc_start: 0.9219 (mm-40) cc_final: 0.9012 (mm-40) REVERT: A 2205 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: A 2306 ASP cc_start: 0.8881 (m-30) cc_final: 0.8661 (m-30) REVERT: A 2310 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8342 (mp0) REVERT: A 2554 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: A 2763 ARG cc_start: 0.7798 (mtt90) cc_final: 0.7206 (mtm110) REVERT: A 3112 LYS cc_start: 0.8349 (mmtm) cc_final: 0.7938 (mmmt) REVERT: A 3969 THR cc_start: 0.8777 (p) cc_final: 0.8514 (p) REVERT: A 4043 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8289 (mtp) REVERT: A 4204 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8377 (mmtm) REVERT: A 4209 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7449 (tp30) outliers start: 47 outliers final: 10 residues processed: 304 average time/residue: 0.7225 time to fit residues: 247.7375 Evaluate side-chains 268 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 253 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4533 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 273 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 180 optimal weight: 0.0040 chunk 278 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1695 HIS A1779 HIS A1985 HIS A2482 GLN A3906 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107428 restraints weight = 28765.578| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.79 r_work: 0.3154 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23529 Z= 0.138 Angle : 0.490 5.921 31915 Z= 0.245 Chirality : 0.040 0.150 3595 Planarity : 0.004 0.047 4090 Dihedral : 7.164 177.304 3175 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.13 % Allowed : 9.28 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.40 (0.16), residues: 2851 helix: 2.38 (0.13), residues: 1646 sheet: -0.25 (0.31), residues: 256 loop : 0.83 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3164 TYR 0.021 0.001 TYR A1546 PHE 0.013 0.001 PHE A1926 TRP 0.019 0.001 TRP A4376 HIS 0.005 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00320 (23529) covalent geometry : angle 0.49049 (31915) hydrogen bonds : bond 0.04002 ( 1374) hydrogen bonds : angle 4.06007 ( 4005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 1683 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: A 2202 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8490 (mtp) REVERT: A 2205 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: A 2306 ASP cc_start: 0.8871 (m-30) cc_final: 0.8643 (m-30) REVERT: A 2310 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8272 (mp0) REVERT: A 2528 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8141 (m) REVERT: A 2615 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8162 (mtt) REVERT: A 2763 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7131 (mtm110) REVERT: A 3112 LYS cc_start: 0.8269 (mmtm) cc_final: 0.7836 (mmmt) REVERT: A 3486 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6223 (ttt180) REVERT: A 3862 ASP cc_start: 0.8329 (m-30) cc_final: 0.8063 (m-30) REVERT: A 3964 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8191 (m) REVERT: A 4043 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8282 (mtp) REVERT: A 4204 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8361 (mmtm) REVERT: A 4209 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7376 (tp30) outliers start: 54 outliers final: 23 residues processed: 305 average time/residue: 0.7535 time to fit residues: 258.2523 Evaluate side-chains 282 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1683 GLU Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2274 GLU Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2528 THR Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3486 ARG Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3964 SER Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4202 SER Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4533 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 181 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 126 optimal weight: 0.0670 chunk 262 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 182 optimal weight: 0.0270 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1653 HIS A1985 HIS A2482 GLN A2827 HIS A3906 GLN A4012 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112027 restraints weight = 29151.805| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.72 r_work: 0.3181 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23529 Z= 0.113 Angle : 0.474 7.408 31915 Z= 0.237 Chirality : 0.039 0.152 3595 Planarity : 0.004 0.049 4090 Dihedral : 6.983 170.843 3175 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.09 % Allowed : 10.03 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.46 (0.16), residues: 2851 helix: 2.43 (0.13), residues: 1651 sheet: -0.28 (0.31), residues: 255 loop : 0.87 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3164 TYR 0.021 0.001 TYR A1546 PHE 0.016 0.001 PHE A1575 TRP 0.019 0.001 TRP A4376 HIS 0.003 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00253 (23529) covalent geometry : angle 0.47431 (31915) hydrogen bonds : bond 0.03736 ( 1374) hydrogen bonds : angle 3.96582 ( 4005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 0.878 Fit side-chains REVERT: A 1643 ASN cc_start: 0.6771 (m-40) cc_final: 0.6554 (m-40) REVERT: A 1683 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8319 (pt0) REVERT: A 1798 MET cc_start: 0.7885 (ptp) cc_final: 0.7583 (ptt) REVERT: A 2202 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8477 (mtm) REVERT: A 2205 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: A 2306 ASP cc_start: 0.8851 (m-30) cc_final: 0.8615 (m-30) REVERT: A 2310 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8292 (mp0) REVERT: A 2528 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8133 (m) REVERT: A 2615 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8140 (mtt) REVERT: A 2763 ARG cc_start: 0.7784 (mtt90) cc_final: 0.7150 (mtm110) REVERT: A 3112 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7822 (mmmt) REVERT: A 3746 GLU cc_start: 0.7631 (tp30) cc_final: 0.7277 (tp30) REVERT: A 3862 ASP cc_start: 0.8347 (m-30) cc_final: 0.8079 (m-30) REVERT: A 3964 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8186 (m) REVERT: A 4043 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8276 (mtp) REVERT: A 4204 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8331 (mmtm) REVERT: A 4209 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: A 4502 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.5808 (tptm) REVERT: A 4633 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7862 (mtm110) outliers start: 53 outliers final: 19 residues processed: 298 average time/residue: 0.7162 time to fit residues: 240.4184 Evaluate side-chains 285 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1683 GLU Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2274 GLU Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2528 THR Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3964 SER Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4301 ARG Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4502 LYS Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4533 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A4062 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105960 restraints weight = 28544.486| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.74 r_work: 0.3124 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23529 Z= 0.201 Angle : 0.541 6.479 31915 Z= 0.270 Chirality : 0.041 0.159 3595 Planarity : 0.004 0.050 4090 Dihedral : 7.119 157.661 3175 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.41 % Allowed : 10.86 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.16), residues: 2851 helix: 2.22 (0.13), residues: 1646 sheet: -0.38 (0.31), residues: 253 loop : 0.80 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A3544 TYR 0.024 0.002 TYR A2472 PHE 0.016 0.002 PHE A3813 TRP 0.024 0.002 TRP A4376 HIS 0.006 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00489 (23529) covalent geometry : angle 0.54115 (31915) hydrogen bonds : bond 0.04376 ( 1374) hydrogen bonds : angle 4.10362 ( 4005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 261 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 1643 ASN cc_start: 0.6748 (m-40) cc_final: 0.6533 (m-40) REVERT: A 1683 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: A 1997 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8027 (pt) REVERT: A 2172 ARG cc_start: 0.7581 (ptm160) cc_final: 0.6884 (tmm-80) REVERT: A 2197 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 2202 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8502 (mtm) REVERT: A 2205 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: A 2306 ASP cc_start: 0.8890 (m-30) cc_final: 0.8688 (m-30) REVERT: A 2310 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8314 (mp0) REVERT: A 2513 GLU cc_start: 0.8112 (tt0) cc_final: 0.7652 (mt-10) REVERT: A 2528 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8223 (m) REVERT: A 2615 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8273 (mtt) REVERT: A 3016 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: A 3112 LYS cc_start: 0.8337 (mmtm) cc_final: 0.7833 (mmmt) REVERT: A 3544 ARG cc_start: 0.8199 (mtm110) cc_final: 0.7517 (mtm110) REVERT: A 3547 ILE cc_start: 0.6263 (tt) cc_final: 0.5983 (tt) REVERT: A 3598 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6855 (mt-10) REVERT: A 3636 GLN cc_start: 0.7145 (pt0) cc_final: 0.6857 (pt0) REVERT: A 3862 ASP cc_start: 0.8268 (m-30) cc_final: 0.7950 (m-30) REVERT: A 3964 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8223 (m) REVERT: A 4043 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: A 4204 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8351 (mmtm) REVERT: A 4209 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: A 4633 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7711 (mtm110) outliers start: 61 outliers final: 25 residues processed: 293 average time/residue: 0.7276 time to fit residues: 239.3285 Evaluate side-chains 284 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1683 GLU Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2197 GLU Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2528 THR Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3964 SER Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4202 SER Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4533 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 104 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 284 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1695 HIS ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2482 GLN A2746 GLN A2827 HIS A3906 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.109080 restraints weight = 28730.465| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.72 r_work: 0.3175 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23529 Z= 0.106 Angle : 0.467 6.048 31915 Z= 0.234 Chirality : 0.038 0.135 3595 Planarity : 0.004 0.049 4090 Dihedral : 6.794 147.773 3175 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.46 % Allowed : 12.36 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.43 (0.16), residues: 2851 helix: 2.41 (0.13), residues: 1647 sheet: -0.25 (0.32), residues: 250 loop : 0.85 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3544 TYR 0.022 0.001 TYR A2472 PHE 0.016 0.001 PHE A1575 TRP 0.023 0.001 TRP A4376 HIS 0.002 0.000 HIS A3907 Details of bonding type rmsd covalent geometry : bond 0.00229 (23529) covalent geometry : angle 0.46709 (31915) hydrogen bonds : bond 0.03682 ( 1374) hydrogen bonds : angle 3.91265 ( 4005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 0.951 Fit side-chains REVERT: A 1997 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8074 (pt) REVERT: A 2180 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: A 2202 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8481 (mtm) REVERT: A 2205 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: A 2306 ASP cc_start: 0.8860 (m-30) cc_final: 0.8648 (m-30) REVERT: A 2310 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8287 (mp0) REVERT: A 2528 THR cc_start: 0.8396 (p) cc_final: 0.8146 (m) REVERT: A 2763 ARG cc_start: 0.7757 (mtt90) cc_final: 0.7132 (mtm110) REVERT: A 3112 LYS cc_start: 0.8351 (mmtm) cc_final: 0.7835 (mmmt) REVERT: A 3501 SER cc_start: 0.7811 (t) cc_final: 0.7573 (m) REVERT: A 3544 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7481 (mtm110) REVERT: A 3547 ILE cc_start: 0.6286 (tt) cc_final: 0.5958 (tt) REVERT: A 3598 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6876 (mt-10) REVERT: A 3746 GLU cc_start: 0.7638 (tp30) cc_final: 0.7383 (tp30) REVERT: A 3862 ASP cc_start: 0.8292 (m-30) cc_final: 0.7975 (m-30) REVERT: A 3964 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.8191 (m) REVERT: A 4043 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8233 (mtp) REVERT: A 4209 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: A 4502 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.5754 (tptm) REVERT: A 4633 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7729 (mtm110) outliers start: 37 outliers final: 15 residues processed: 288 average time/residue: 0.6874 time to fit residues: 223.3766 Evaluate side-chains 276 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2274 GLU Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3964 SER Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4301 ARG Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4502 LYS Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4533 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 115 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 271 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 225 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 240 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A3906 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111823 restraints weight = 29255.449| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.68 r_work: 0.3174 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23529 Z= 0.114 Angle : 0.468 6.226 31915 Z= 0.235 Chirality : 0.038 0.157 3595 Planarity : 0.004 0.049 4090 Dihedral : 6.605 136.854 3175 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.94 % Allowed : 12.48 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.51 (0.16), residues: 2851 helix: 2.45 (0.13), residues: 1651 sheet: -0.22 (0.32), residues: 240 loop : 0.90 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3078 TYR 0.024 0.001 TYR A2472 PHE 0.016 0.001 PHE A1575 TRP 0.028 0.001 TRP A4376 HIS 0.002 0.001 HIS A4508 Details of bonding type rmsd covalent geometry : bond 0.00255 (23529) covalent geometry : angle 0.46837 (31915) hydrogen bonds : bond 0.03671 ( 1374) hydrogen bonds : angle 3.86720 ( 4005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 0.858 Fit side-chains REVERT: A 1798 MET cc_start: 0.7992 (ptp) cc_final: 0.7675 (ptt) REVERT: A 2180 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 2202 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8491 (mtm) REVERT: A 2205 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: A 2306 ASP cc_start: 0.8844 (m-30) cc_final: 0.8634 (m-30) REVERT: A 2310 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8333 (mp0) REVERT: A 2528 THR cc_start: 0.8377 (p) cc_final: 0.8140 (m) REVERT: A 3032 GLN cc_start: 0.8347 (mt0) cc_final: 0.8139 (mt0) REVERT: A 3112 LYS cc_start: 0.8346 (mmtm) cc_final: 0.7830 (mmmt) REVERT: A 3501 SER cc_start: 0.7834 (t) cc_final: 0.7621 (m) REVERT: A 3544 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7708 (mtm110) REVERT: A 3547 ILE cc_start: 0.6403 (tt) cc_final: 0.6123 (tt) REVERT: A 3598 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6934 (mt-10) REVERT: A 3751 GLN cc_start: 0.7476 (tt0) cc_final: 0.7233 (tt0) REVERT: A 3862 ASP cc_start: 0.8356 (m-30) cc_final: 0.8034 (m-30) REVERT: A 3964 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8219 (m) REVERT: A 4043 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8238 (mtp) REVERT: A 4204 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8318 (mmtm) REVERT: A 4209 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: A 4502 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.5736 (tptm) REVERT: A 4630 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 4633 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7770 (mtm110) outliers start: 49 outliers final: 21 residues processed: 288 average time/residue: 0.7094 time to fit residues: 229.4411 Evaluate side-chains 278 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2274 GLU Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3930 GLU Chi-restraints excluded: chain A residue 3964 SER Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4301 ARG Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4502 LYS Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4630 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 4 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2482 GLN A3906 GLN A4258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109769 restraints weight = 29333.550| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.70 r_work: 0.3148 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23529 Z= 0.154 Angle : 0.504 6.534 31915 Z= 0.252 Chirality : 0.040 0.158 3595 Planarity : 0.004 0.049 4090 Dihedral : 6.623 128.695 3175 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.01 % Allowed : 12.60 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.16), residues: 2851 helix: 2.36 (0.13), residues: 1652 sheet: -0.17 (0.32), residues: 239 loop : 0.84 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3078 TYR 0.023 0.001 TYR A2472 PHE 0.020 0.001 PHE A1575 TRP 0.030 0.001 TRP A4376 HIS 0.003 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00367 (23529) covalent geometry : angle 0.50361 (31915) hydrogen bonds : bond 0.03945 ( 1374) hydrogen bonds : angle 3.93365 ( 4005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 1798 MET cc_start: 0.8003 (ptp) cc_final: 0.7685 (ptt) REVERT: A 1997 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8077 (pt) REVERT: A 2202 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: A 2205 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: A 2310 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8312 (mp0) REVERT: A 2513 GLU cc_start: 0.8148 (tt0) cc_final: 0.7707 (mt-10) REVERT: A 2528 THR cc_start: 0.8413 (p) cc_final: 0.8180 (m) REVERT: A 2763 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7176 (mtm110) REVERT: A 3032 GLN cc_start: 0.8360 (mt0) cc_final: 0.8154 (mt0) REVERT: A 3112 LYS cc_start: 0.8349 (mmtm) cc_final: 0.7842 (mmmt) REVERT: A 3501 SER cc_start: 0.7886 (t) cc_final: 0.7680 (m) REVERT: A 3544 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7701 (mtm110) REVERT: A 3547 ILE cc_start: 0.6420 (tt) cc_final: 0.6100 (tt) REVERT: A 3598 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6922 (mt-10) REVERT: A 3862 ASP cc_start: 0.8342 (m-30) cc_final: 0.8007 (m-30) REVERT: A 3964 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8235 (m) REVERT: A 4043 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8273 (mtp) REVERT: A 4092 ARG cc_start: 0.8369 (mtm180) cc_final: 0.8038 (mtp85) REVERT: A 4204 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8310 (mmtm) REVERT: A 4209 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: A 4502 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.5761 (tptm) REVERT: A 4630 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 4633 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7845 (mtm110) outliers start: 51 outliers final: 27 residues processed: 286 average time/residue: 0.6973 time to fit residues: 225.1038 Evaluate side-chains 284 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2274 GLU Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2882 ILE Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3930 GLU Chi-restraints excluded: chain A residue 3964 SER Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4202 SER Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4301 ARG Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4502 LYS Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4630 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 248 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 97 optimal weight: 0.0370 chunk 103 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 chunk 215 optimal weight: 0.0870 chunk 279 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2827 HIS A3499 GLN A3563 GLN A3906 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113158 restraints weight = 29263.555| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.75 r_work: 0.3204 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23529 Z= 0.097 Angle : 0.466 7.027 31915 Z= 0.233 Chirality : 0.038 0.155 3595 Planarity : 0.004 0.049 4090 Dihedral : 6.294 116.895 3175 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.74 % Allowed : 13.39 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.16), residues: 2851 helix: 2.52 (0.13), residues: 1655 sheet: -0.15 (0.32), residues: 247 loop : 0.98 (0.22), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3164 TYR 0.024 0.001 TYR A2472 PHE 0.021 0.001 PHE A1575 TRP 0.035 0.001 TRP A4376 HIS 0.002 0.000 HIS A3188 Details of bonding type rmsd covalent geometry : bond 0.00204 (23529) covalent geometry : angle 0.46566 (31915) hydrogen bonds : bond 0.03443 ( 1374) hydrogen bonds : angle 3.79563 ( 4005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.793 Fit side-chains REVERT: A 1798 MET cc_start: 0.8009 (ptp) cc_final: 0.7703 (ptt) REVERT: A 1997 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8128 (pt) REVERT: A 2180 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: A 2202 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8502 (mtm) REVERT: A 2205 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: A 2310 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8355 (mp0) REVERT: A 2528 THR cc_start: 0.8374 (p) cc_final: 0.8163 (m) REVERT: A 2561 LYS cc_start: 0.8417 (mttt) cc_final: 0.7926 (mtpt) REVERT: A 2763 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7163 (mtm110) REVERT: A 3112 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7829 (mmmt) REVERT: A 3199 MET cc_start: 0.6959 (ttt) cc_final: 0.6670 (ttm) REVERT: A 3544 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7732 (mtm110) REVERT: A 3547 ILE cc_start: 0.6437 (tt) cc_final: 0.6113 (tt) REVERT: A 3862 ASP cc_start: 0.8365 (m-30) cc_final: 0.8014 (m-30) REVERT: A 3964 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8198 (m) REVERT: A 4043 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8157 (mtp) REVERT: A 4092 ARG cc_start: 0.8343 (mtm180) cc_final: 0.8028 (mtp85) REVERT: A 4209 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 4476 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8167 (mm) REVERT: A 4502 LYS cc_start: 0.6381 (OUTLIER) cc_final: 0.5648 (tptm) REVERT: A 4630 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: A 4633 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.6568 (mmt180) outliers start: 44 outliers final: 19 residues processed: 301 average time/residue: 0.6927 time to fit residues: 235.9496 Evaluate side-chains 280 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2180 GLU Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2274 GLU Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3964 SER Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4502 LYS Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4630 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 174 optimal weight: 4.9990 chunk 268 optimal weight: 0.0470 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 63 optimal weight: 0.0020 chunk 109 optimal weight: 0.0270 chunk 43 optimal weight: 0.3980 chunk 196 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 283 optimal weight: 0.7980 overall best weight: 0.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2827 HIS A3499 GLN A3906 GLN A4012 ASN A4117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112266 restraints weight = 28710.306| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.75 r_work: 0.3220 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23529 Z= 0.094 Angle : 0.464 7.869 31915 Z= 0.231 Chirality : 0.038 0.134 3595 Planarity : 0.004 0.049 4090 Dihedral : 6.071 113.555 3175 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.22 % Allowed : 14.02 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.68 (0.16), residues: 2851 helix: 2.59 (0.13), residues: 1656 sheet: -0.27 (0.32), residues: 250 loop : 1.01 (0.22), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3078 TYR 0.023 0.001 TYR A2472 PHE 0.018 0.001 PHE A1575 TRP 0.035 0.001 TRP A4376 HIS 0.002 0.000 HIS A3188 Details of bonding type rmsd covalent geometry : bond 0.00197 (23529) covalent geometry : angle 0.46434 (31915) hydrogen bonds : bond 0.03342 ( 1374) hydrogen bonds : angle 3.72740 ( 4005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 1790 ASN cc_start: 0.7949 (m-40) cc_final: 0.7741 (t0) REVERT: A 1798 MET cc_start: 0.8007 (ptp) cc_final: 0.7726 (ptt) REVERT: A 1997 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8089 (pt) REVERT: A 2074 LYS cc_start: 0.8399 (tmtp) cc_final: 0.7612 (ttmt) REVERT: A 2202 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8470 (mtm) REVERT: A 2205 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: A 2310 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8326 (mp0) REVERT: A 3112 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7836 (mmmt) REVERT: A 3199 MET cc_start: 0.6948 (ttt) cc_final: 0.6655 (ttm) REVERT: A 3544 ARG cc_start: 0.8044 (mtm110) cc_final: 0.7685 (mtm110) REVERT: A 3547 ILE cc_start: 0.6458 (tt) cc_final: 0.6114 (tt) REVERT: A 3862 ASP cc_start: 0.8370 (m-30) cc_final: 0.8016 (m-30) REVERT: A 3962 ASP cc_start: 0.8184 (m-30) cc_final: 0.7717 (p0) REVERT: A 3964 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8194 (m) REVERT: A 4043 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: A 4092 ARG cc_start: 0.8354 (mtm180) cc_final: 0.8038 (mtp85) REVERT: A 4209 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: A 4502 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5539 (tptm) REVERT: A 4630 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: A 4633 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.6549 (mmt180) outliers start: 31 outliers final: 15 residues processed: 282 average time/residue: 0.7461 time to fit residues: 236.6749 Evaluate side-chains 275 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3964 SER Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4502 LYS Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4533 SER Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4630 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 212 optimal weight: 0.5980 chunk 205 optimal weight: 0.5980 chunk 254 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 0.0970 chunk 136 optimal weight: 0.7980 chunk 225 optimal weight: 0.2980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A3499 GLN A3906 GLN A4012 ASN A4572 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110282 restraints weight = 28740.658| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.69 r_work: 0.3224 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23529 Z= 0.100 Angle : 0.475 11.625 31915 Z= 0.235 Chirality : 0.038 0.308 3595 Planarity : 0.004 0.050 4090 Dihedral : 6.025 112.300 3175 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.34 % Allowed : 14.26 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.71 (0.16), residues: 2851 helix: 2.62 (0.13), residues: 1655 sheet: -0.24 (0.32), residues: 253 loop : 1.03 (0.22), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3164 TYR 0.024 0.001 TYR A2472 PHE 0.020 0.001 PHE A1575 TRP 0.034 0.001 TRP A4376 HIS 0.002 0.000 HIS A3188 Details of bonding type rmsd covalent geometry : bond 0.00220 (23529) covalent geometry : angle 0.47497 (31915) hydrogen bonds : bond 0.03378 ( 1374) hydrogen bonds : angle 3.71812 ( 4005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8581.28 seconds wall clock time: 146 minutes 25.54 seconds (8785.54 seconds total)