Starting phenix.real_space_refine on Thu May 22 21:44:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm2_44685/05_2025/9bm2_44685.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm2_44685/05_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_44685/05_2025/9bm2_44685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm2_44685/05_2025/9bm2_44685.map" model { file = "/net/cci-nas-00/data/ceres_data/9bm2_44685/05_2025/9bm2_44685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm2_44685/05_2025/9bm2_44685.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.00, per 1000 atoms: 0.52 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: 5.81 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 4.14 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: 14.81 Time building geometry restraints manager: 6.80 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 57.710 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.022 0.001 TRP A1701 HIS 0.006 0.001 HIS A1810 PHE 0.016 0.001 PHE A1926 TYR 0.027 0.001 TYR A1546 ARG 0.009 0.000 ARG A1966 Details of bonding type rmsd hydrogen bonds : bond 0.12327 ( 1374) hydrogen bonds : angle 5.33920 ( 4005) covalent geometry : bond 0.00391 (23529) covalent geometry : angle 0.63065 (31915) *********************** 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 : 2.637 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: 1.6066 time to fit residues: 713.9360 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 : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 1.9990 chunk 216 optimal weight: 0.0270 chunk 119 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 0.0770 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 HIS ** A1856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 ASN A2187 GLN A2482 GLN A2621 ASN A2827 HIS A3032 GLN A3069 ASN A3906 GLN A4098 ASN A4231 GLN A4466 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115691 restraints weight = 28524.022| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.69 r_work: 0.3218 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23529 Z= 0.114 Angle : 0.491 7.532 31915 Z= 0.248 Chirality : 0.039 0.146 3595 Planarity : 0.004 0.045 4090 Dihedral : 7.229 175.339 3175 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.86 % Allowed : 7.50 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.16), residues: 2851 helix: 2.36 (0.13), residues: 1654 sheet: -0.26 (0.32), residues: 255 loop : 0.91 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.004 0.001 HIS A1810 PHE 0.015 0.001 PHE A1575 TYR 0.023 0.001 TYR A1546 ARG 0.005 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1374) hydrogen bonds : angle 4.20095 ( 4005) covalent geometry : bond 0.00241 (23529) covalent geometry : angle 0.49120 (31915) *********************** 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 330 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 2.421 Fit side-chains REVERT: A 1950 GLN cc_start: 0.9213 (mm-40) cc_final: 0.9005 (mm-40) REVERT: A 2205 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: A 2306 ASP cc_start: 0.8898 (m-30) cc_final: 0.8684 (m-30) REVERT: A 2310 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8348 (mp0) REVERT: A 2554 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: A 2763 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7187 (mtm110) REVERT: A 3112 LYS cc_start: 0.8345 (mmtm) cc_final: 0.7937 (mmmt) REVERT: A 3969 THR cc_start: 0.8776 (p) cc_final: 0.8510 (p) REVERT: A 4043 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8283 (mtp) REVERT: A 4204 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8371 (mmtm) REVERT: A 4209 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7462 (tp30) outliers start: 47 outliers final: 10 residues processed: 307 average time/residue: 1.5514 time to fit residues: 538.9400 Evaluate side-chains 271 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 256 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 269 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 240 optimal weight: 0.0980 chunk 272 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 220 optimal weight: 0.0570 chunk 209 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- 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 A2827 HIS A3906 GLN A4258 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115026 restraints weight = 28458.105| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.72 r_work: 0.3225 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23529 Z= 0.107 Angle : 0.467 5.898 31915 Z= 0.234 Chirality : 0.038 0.135 3595 Planarity : 0.004 0.047 4090 Dihedral : 7.083 178.630 3175 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.86 % Allowed : 9.40 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.16), residues: 2851 helix: 2.43 (0.13), residues: 1658 sheet: -0.23 (0.31), residues: 256 loop : 0.87 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4376 HIS 0.004 0.001 HIS A1810 PHE 0.012 0.001 PHE A1575 TYR 0.021 0.001 TYR A1546 ARG 0.009 0.000 ARG A3167 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 1374) hydrogen bonds : angle 4.00285 ( 4005) covalent geometry : bond 0.00232 (23529) covalent geometry : angle 0.46713 (31915) *********************** 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 322 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 2.406 Fit side-chains revert: symmetry clash REVERT: A 1643 ASN cc_start: 0.6782 (m-40) cc_final: 0.6555 (m-40) REVERT: A 1683 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: A 2202 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8458 (mtm) REVERT: A 2205 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: A 2306 ASP cc_start: 0.8911 (m-30) cc_final: 0.8676 (m-30) REVERT: A 2310 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8319 (mp0) REVERT: A 2528 THR cc_start: 0.8360 (p) cc_final: 0.8114 (m) REVERT: A 2606 PHE cc_start: 0.8622 (m-10) cc_final: 0.8362 (m-10) REVERT: A 2615 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8108 (mtt) REVERT: A 2763 ARG cc_start: 0.7752 (mtt90) cc_final: 0.7152 (mtm110) REVERT: A 2996 GLU cc_start: 0.8119 (pt0) cc_final: 0.7775 (pt0) REVERT: A 3016 GLU cc_start: 0.8567 (pp20) cc_final: 0.8357 (pm20) REVERT: A 3112 LYS cc_start: 0.8271 (mmtm) cc_final: 0.7840 (mmmt) REVERT: A 3486 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.6273 (ttt180) REVERT: A 3544 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7656 (mtm110) REVERT: A 3746 GLU cc_start: 0.7504 (tp30) cc_final: 0.7253 (tp30) REVERT: A 3862 ASP cc_start: 0.8381 (m-30) cc_final: 0.8126 (m-30) REVERT: A 4043 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8253 (mtp) REVERT: A 4204 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8355 (mmtm) REVERT: A 4209 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: A 4502 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.5857 (tptm) outliers start: 47 outliers final: 15 residues processed: 304 average time/residue: 1.5427 time to fit residues: 532.3650 Evaluate side-chains 278 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 2.471 ------------------------------------------------------------------------------- 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 2175 MET 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 2334 SER Chi-restraints excluded: chain A residue 2448 ASP 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 3486 ARG Chi-restraints excluded: chain A residue 3612 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 185 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 258 optimal weight: 0.0170 chunk 169 optimal weight: 7.9990 chunk 256 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1985 HIS A2482 GLN A2827 HIS A3906 GLN A4012 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111888 restraints weight = 29216.716| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.72 r_work: 0.3175 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23529 Z= 0.126 Angle : 0.480 8.006 31915 Z= 0.239 Chirality : 0.039 0.145 3595 Planarity : 0.004 0.048 4090 Dihedral : 6.929 168.637 3175 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.05 % Allowed : 9.95 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.16), residues: 2851 helix: 2.44 (0.13), residues: 1655 sheet: -0.25 (0.31), residues: 254 loop : 0.87 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A4376 HIS 0.004 0.001 HIS A1810 PHE 0.012 0.001 PHE A1575 TYR 0.022 0.001 TYR A2472 ARG 0.008 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 1374) hydrogen bonds : angle 3.94435 ( 4005) covalent geometry : bond 0.00289 (23529) covalent geometry : angle 0.47982 (31915) *********************** 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 315 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 2.704 Fit side-chains REVERT: A 1683 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: A 1798 MET cc_start: 0.7870 (ptp) cc_final: 0.7573 (ptt) REVERT: A 2202 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8475 (mtm) REVERT: A 2205 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: A 2306 ASP cc_start: 0.8846 (m-30) cc_final: 0.8604 (m-30) REVERT: A 2310 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8293 (mp0) REVERT: A 2510 MET cc_start: 0.8756 (mmt) cc_final: 0.8471 (mmt) REVERT: A 2528 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8121 (m) REVERT: A 2615 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8108 (mtt) REVERT: A 2763 ARG cc_start: 0.7774 (mtt90) cc_final: 0.7140 (mtm110) REVERT: A 2811 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7622 (mtt-85) REVERT: A 3016 GLU cc_start: 0.8635 (pp20) cc_final: 0.8421 (pm20) REVERT: A 3112 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7808 (mmmt) REVERT: A 3544 ARG cc_start: 0.8183 (ttm110) cc_final: 0.7712 (mtm110) REVERT: A 3547 ILE cc_start: 0.6420 (tt) cc_final: 0.6164 (tt) REVERT: A 3862 ASP cc_start: 0.8360 (m-30) cc_final: 0.8083 (m-30) REVERT: A 3964 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8189 (m) REVERT: A 4043 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: A 4204 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8346 (mmtm) REVERT: A 4209 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: A 4633 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7776 (mtm110) outliers start: 52 outliers final: 20 residues processed: 293 average time/residue: 1.6220 time to fit residues: 536.0374 Evaluate side-chains 289 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2175 MET 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 71 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 A3906 GLN A4062 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107466 restraints weight = 28779.295| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.75 r_work: 0.3149 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23529 Z= 0.165 Angle : 0.503 6.011 31915 Z= 0.251 Chirality : 0.040 0.152 3595 Planarity : 0.004 0.050 4090 Dihedral : 6.937 156.940 3175 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.37 % Allowed : 10.43 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.16), residues: 2851 helix: 2.35 (0.13), residues: 1649 sheet: -0.20 (0.32), residues: 249 loop : 0.82 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4376 HIS 0.004 0.001 HIS A1810 PHE 0.013 0.002 PHE A3813 TYR 0.022 0.001 TYR A2472 ARG 0.006 0.000 ARG A3078 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 1374) hydrogen bonds : angle 3.99341 ( 4005) covalent geometry : bond 0.00394 (23529) covalent geometry : angle 0.50280 (31915) *********************** 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 325 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 2.667 Fit side-chains REVERT: A 2202 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8489 (mtm) REVERT: A 2205 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: A 2306 ASP cc_start: 0.8867 (m-30) cc_final: 0.8646 (m-30) REVERT: A 2310 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8280 (mp0) REVERT: A 2510 MET cc_start: 0.8820 (mmt) cc_final: 0.8550 (mmt) REVERT: A 2528 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8160 (m) REVERT: A 3032 GLN cc_start: 0.8286 (mt0) cc_final: 0.8072 (mt0) REVERT: A 3112 LYS cc_start: 0.8330 (mmtm) cc_final: 0.7824 (mmmt) REVERT: A 3544 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7674 (mtm110) REVERT: A 3547 ILE cc_start: 0.6541 (tt) cc_final: 0.6263 (tt) REVERT: A 3598 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6878 (mt-10) REVERT: A 3862 ASP cc_start: 0.8336 (m-30) cc_final: 0.8008 (m-30) REVERT: A 3964 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8232 (m) REVERT: A 4043 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8243 (mtp) REVERT: A 4204 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8308 (mmtm) REVERT: A 4209 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: A 4502 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.5737 (tptm) REVERT: A 4633 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7727 (mtm110) outliers start: 60 outliers final: 28 residues processed: 299 average time/residue: 1.5433 time to fit residues: 526.4521 Evaluate side-chains 286 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1709 MET 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 2138 ILE Chi-restraints excluded: chain A residue 2170 TYR 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 11 optimal weight: 0.0040 chunk 113 optimal weight: 2.9990 chunk 216 optimal weight: 0.4980 chunk 217 optimal weight: 5.9990 chunk 253 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 276 optimal weight: 0.0270 overall best weight: 0.5052 ------------------------------------------------------------------------------- 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 A3563 GLN A3906 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.109079 restraints weight = 28551.485| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.65 r_work: 0.3200 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23529 Z= 0.100 Angle : 0.458 6.034 31915 Z= 0.229 Chirality : 0.038 0.134 3595 Planarity : 0.004 0.049 4090 Dihedral : 6.647 146.566 3175 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.70 % Allowed : 11.81 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.16), residues: 2851 helix: 2.49 (0.13), residues: 1654 sheet: -0.19 (0.32), residues: 249 loop : 0.86 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4376 HIS 0.002 0.000 HIS A3188 PHE 0.015 0.001 PHE A1575 TYR 0.023 0.001 TYR A2472 ARG 0.007 0.000 ARG A3078 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 1374) hydrogen bonds : angle 3.84865 ( 4005) covalent geometry : bond 0.00215 (23529) covalent geometry : angle 0.45797 (31915) *********************** 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 316 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 2.472 Fit side-chains REVERT: A 1643 ASN cc_start: 0.6604 (m-40) cc_final: 0.6348 (m-40) REVERT: A 1798 MET cc_start: 0.7979 (ptp) cc_final: 0.7688 (ptt) REVERT: A 1997 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8072 (pt) REVERT: A 2180 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: A 2202 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8488 (mtm) REVERT: A 2205 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: A 2306 ASP cc_start: 0.8828 (m-30) cc_final: 0.8592 (m-30) REVERT: A 2310 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8309 (mp0) REVERT: A 2528 THR cc_start: 0.8361 (p) cc_final: 0.8121 (m) REVERT: A 2606 PHE cc_start: 0.8620 (m-10) cc_final: 0.8383 (m-10) REVERT: A 2763 ARG cc_start: 0.7750 (mtt90) cc_final: 0.7147 (mtm110) REVERT: A 3032 GLN cc_start: 0.8219 (mt0) cc_final: 0.7995 (mt0) REVERT: A 3112 LYS cc_start: 0.8346 (mmtm) cc_final: 0.7848 (mmmt) REVERT: A 3501 SER cc_start: 0.7783 (t) cc_final: 0.7557 (m) REVERT: A 3544 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7682 (mtm110) REVERT: A 3547 ILE cc_start: 0.6577 (tt) cc_final: 0.6263 (tt) REVERT: A 3862 ASP cc_start: 0.8345 (m-30) cc_final: 0.8034 (m-30) REVERT: A 3964 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8246 (m) REVERT: A 4043 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8209 (mtp) REVERT: A 4209 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: A 4502 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.5672 (tptm) REVERT: A 4633 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7759 (mtm110) outliers start: 43 outliers final: 16 residues processed: 299 average time/residue: 1.5431 time to fit residues: 522.5236 Evaluate side-chains 278 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 ILE Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1824 SER 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 2448 ASP Chi-restraints excluded: chain A residue 2627 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 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 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107595 restraints weight = 28889.228| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.71 r_work: 0.3153 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23529 Z= 0.155 Angle : 0.504 6.766 31915 Z= 0.251 Chirality : 0.040 0.148 3595 Planarity : 0.004 0.050 4090 Dihedral : 6.661 136.286 3175 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.97 % Allowed : 12.28 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.16), residues: 2851 helix: 2.39 (0.13), residues: 1653 sheet: -0.21 (0.32), residues: 249 loop : 0.82 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A4376 HIS 0.004 0.001 HIS A4508 PHE 0.013 0.001 PHE A3813 TYR 0.023 0.001 TYR A2472 ARG 0.006 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 1374) hydrogen bonds : angle 3.92468 ( 4005) covalent geometry : bond 0.00369 (23529) covalent geometry : angle 0.50397 (31915) *********************** 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 311 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 2.460 Fit side-chains REVERT: A 1641 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6826 (mt) REVERT: A 1997 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7997 (pt) REVERT: A 2202 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8491 (mtm) REVERT: A 2205 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: A 2306 ASP cc_start: 0.8875 (m-30) cc_final: 0.8664 (m-30) REVERT: A 2310 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8297 (mp0) REVERT: A 2513 GLU cc_start: 0.8127 (tt0) cc_final: 0.7678 (mt-10) REVERT: A 2528 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8156 (m) REVERT: A 2763 ARG cc_start: 0.7743 (mtt90) cc_final: 0.7107 (mtm110) REVERT: A 3032 GLN cc_start: 0.8208 (mt0) cc_final: 0.8003 (mt0) REVERT: A 3112 LYS cc_start: 0.8343 (mmtm) cc_final: 0.7821 (mmmt) REVERT: A 3544 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7626 (mtm110) REVERT: A 3547 ILE cc_start: 0.6508 (tt) cc_final: 0.6194 (tt) REVERT: A 3598 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6830 (mt-10) REVERT: A 3862 ASP cc_start: 0.8319 (m-30) cc_final: 0.7958 (m-30) REVERT: A 3964 SER cc_start: 0.8469 (OUTLIER) cc_final: 0.8202 (m) REVERT: A 4043 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8268 (mtp) REVERT: A 4204 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8306 (mmtm) REVERT: A 4209 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: A 4502 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.5700 (tptm) REVERT: A 4630 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: A 4633 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7748 (mtm110) outliers start: 50 outliers final: 22 residues processed: 291 average time/residue: 1.5971 time to fit residues: 530.8990 Evaluate side-chains 285 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1666 LEU 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 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2267 THR 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 2627 THR Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3199 MET Chi-restraints excluded: chain A residue 3612 THR 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 4630 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 220 optimal weight: 0.0470 chunk 100 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 142 optimal weight: 1.9990 chunk 262 optimal weight: 0.4980 chunk 184 optimal weight: 0.0010 chunk 31 optimal weight: 0.3980 overall best weight: 0.2684 ------------------------------------------------------------------------------- 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 A2827 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111401 restraints weight = 28588.184| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.80 r_work: 0.3201 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23529 Z= 0.093 Angle : 0.460 7.871 31915 Z= 0.230 Chirality : 0.038 0.134 3595 Planarity : 0.004 0.048 4090 Dihedral : 6.288 121.494 3175 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.66 % Allowed : 12.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.16), residues: 2851 helix: 2.57 (0.13), residues: 1653 sheet: -0.23 (0.32), residues: 254 loop : 0.96 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A4376 HIS 0.002 0.000 HIS A2445 PHE 0.015 0.001 PHE A1575 TYR 0.024 0.001 TYR A2472 ARG 0.007 0.000 ARG A3078 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 1374) hydrogen bonds : angle 3.77050 ( 4005) covalent geometry : bond 0.00192 (23529) covalent geometry : angle 0.45986 (31915) *********************** 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 306 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 2.629 Fit side-chains REVERT: A 1798 MET cc_start: 0.7948 (ptp) cc_final: 0.7645 (ptt) REVERT: A 1997 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8046 (pt) REVERT: A 2074 LYS cc_start: 0.8370 (tmtp) cc_final: 0.7675 (ttmt) REVERT: A 2205 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: A 2306 ASP cc_start: 0.8823 (m-30) cc_final: 0.8590 (m-30) REVERT: A 2310 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8290 (mp0) REVERT: A 2528 THR cc_start: 0.8369 (p) cc_final: 0.8149 (m) REVERT: A 3032 GLN cc_start: 0.8113 (mt0) cc_final: 0.7897 (mt0) REVERT: A 3112 LYS cc_start: 0.8280 (mmtm) cc_final: 0.7811 (mmmt) REVERT: A 3199 MET cc_start: 0.6897 (ttt) cc_final: 0.6583 (ttm) REVERT: A 3506 ASP cc_start: 0.8333 (m-30) cc_final: 0.8112 (m-30) REVERT: A 3544 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7673 (mtm110) REVERT: A 3547 ILE cc_start: 0.6517 (tt) cc_final: 0.6176 (tt) REVERT: A 3862 ASP cc_start: 0.8382 (m-30) cc_final: 0.8023 (m-30) REVERT: A 3964 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8179 (m) REVERT: A 4043 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8134 (mtp) REVERT: A 4209 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: A 4476 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 4502 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5597 (tptm) REVERT: A 4633 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.6509 (mmt180) outliers start: 42 outliers final: 16 residues processed: 290 average time/residue: 1.5322 time to fit residues: 505.1804 Evaluate side-chains 273 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1641 ILE 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 1997 ILE 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 3635 VAL Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3912 ASN 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 4340 ILE 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 4533 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 72 optimal weight: 0.0170 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 0.0060 chunk 218 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.4212 ------------------------------------------------------------------------------- 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 A2827 HIS 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 = 0.3702 r_free = 0.3702 target = 0.143206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111581 restraints weight = 28747.382| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.71 r_work: 0.3211 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23529 Z= 0.098 Angle : 0.466 6.894 31915 Z= 0.232 Chirality : 0.038 0.171 3595 Planarity : 0.004 0.050 4090 Dihedral : 6.171 117.545 3175 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.38 % Allowed : 13.11 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.16), residues: 2851 helix: 2.61 (0.13), residues: 1652 sheet: -0.26 (0.32), residues: 254 loop : 0.99 (0.22), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A4376 HIS 0.002 0.000 HIS A3188 PHE 0.026 0.001 PHE A1575 TYR 0.024 0.001 TYR A2472 ARG 0.007 0.000 ARG A3078 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 1374) hydrogen bonds : angle 3.74832 ( 4005) covalent geometry : bond 0.00211 (23529) covalent geometry : angle 0.46623 (31915) *********************** 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 295 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 2.436 Fit side-chains revert: symmetry clash REVERT: A 1798 MET cc_start: 0.8009 (ptp) cc_final: 0.7671 (ptt) REVERT: A 1997 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8074 (pt) REVERT: A 2074 LYS cc_start: 0.8433 (tmtp) cc_final: 0.7761 (ttmt) REVERT: A 2202 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: A 2205 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: A 2306 ASP cc_start: 0.8830 (m-30) cc_final: 0.8600 (m-30) REVERT: A 2310 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8303 (mp0) REVERT: A 3032 GLN cc_start: 0.8157 (mt0) cc_final: 0.7935 (mt0) REVERT: A 3112 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7856 (mmmt) REVERT: A 3199 MET cc_start: 0.6917 (ttt) cc_final: 0.6606 (ttm) REVERT: A 3506 ASP cc_start: 0.8366 (m-30) cc_final: 0.8156 (m-30) REVERT: A 3544 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7710 (mtm110) REVERT: A 3547 ILE cc_start: 0.6595 (tt) cc_final: 0.6246 (tt) REVERT: A 3862 ASP cc_start: 0.8360 (m-30) cc_final: 0.8016 (m-30) REVERT: A 3964 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8188 (m) REVERT: A 4043 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8119 (mtp) REVERT: A 4209 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: A 4502 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5604 (tptm) REVERT: A 4633 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.6562 (mmt180) outliers start: 35 outliers final: 21 residues processed: 284 average time/residue: 1.5290 time to fit residues: 499.7273 Evaluate side-chains 275 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1824 SER 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 2353 LEU 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 2968 THR Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3912 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 128 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 151 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 280 optimal weight: 0.0970 chunk 162 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5956 ------------------------------------------------------------------------------- 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** A3906 GLN A4117 GLN A4572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111599 restraints weight = 28765.500| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.77 r_work: 0.3201 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23529 Z= 0.104 Angle : 0.470 7.420 31915 Z= 0.233 Chirality : 0.038 0.134 3595 Planarity : 0.004 0.051 4090 Dihedral : 6.111 114.595 3175 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.26 % Allowed : 13.67 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.16), residues: 2851 helix: 2.59 (0.13), residues: 1653 sheet: -0.27 (0.32), residues: 254 loop : 1.00 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A4376 HIS 0.004 0.001 HIS A2445 PHE 0.018 0.001 PHE A1575 TYR 0.023 0.001 TYR A2472 ARG 0.007 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 1374) hydrogen bonds : angle 3.75601 ( 4005) covalent geometry : bond 0.00231 (23529) covalent geometry : angle 0.46968 (31915) ********************** 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 283 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 2.693 Fit side-chains revert: symmetry clash REVERT: A 1798 MET cc_start: 0.8033 (ptp) cc_final: 0.7687 (ptt) REVERT: A 1997 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8078 (pt) REVERT: A 2074 LYS cc_start: 0.8423 (tmtp) cc_final: 0.7760 (ttmt) REVERT: A 2202 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8501 (mtm) REVERT: A 2205 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: A 2306 ASP cc_start: 0.8826 (m-30) cc_final: 0.8602 (m-30) REVERT: A 2310 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8284 (mp0) REVERT: A 3032 GLN cc_start: 0.8148 (mt0) cc_final: 0.7927 (mt0) REVERT: A 3112 LYS cc_start: 0.8337 (mmtm) cc_final: 0.7864 (mmmt) REVERT: A 3199 MET cc_start: 0.6921 (ttt) cc_final: 0.6606 (ttm) REVERT: A 3506 ASP cc_start: 0.8367 (m-30) cc_final: 0.8158 (m-30) REVERT: A 3544 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7686 (mtm110) REVERT: A 3547 ILE cc_start: 0.6591 (tt) cc_final: 0.6245 (tt) REVERT: A 3862 ASP cc_start: 0.8349 (m-30) cc_final: 0.8000 (m-30) REVERT: A 3964 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8190 (m) REVERT: A 4043 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8140 (mtp) REVERT: A 4209 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: A 4502 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5563 (tptm) REVERT: A 4633 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.6562 (mmt180) outliers start: 32 outliers final: 20 residues processed: 272 average time/residue: 1.5420 time to fit residues: 476.4795 Evaluate side-chains 275 residues out of total 2532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1737 THR Chi-restraints excluded: chain A residue 1824 SER 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 2353 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3912 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 199 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 166 optimal weight: 0.0170 chunk 169 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 A4117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111048 restraints weight = 28621.822| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.75 r_work: 0.3195 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2020 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= 0.111 Angle : 0.483 11.629 31915 Z= 0.240 Chirality : 0.039 0.272 3595 Planarity : 0.004 0.051 4090 Dihedral : 6.094 112.306 3175 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.30 % Allowed : 13.78 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.16), residues: 2851 helix: 2.58 (0.13), residues: 1652 sheet: -0.21 (0.33), residues: 244 loop : 0.99 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A4376 HIS 0.003 0.001 HIS A2445 PHE 0.021 0.001 PHE A1575 TYR 0.023 0.001 TYR A2472 ARG 0.007 0.000 ARG A3078 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 1374) hydrogen bonds : angle 3.77701 ( 4005) covalent geometry : bond 0.00251 (23529) covalent geometry : angle 0.48299 (31915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18281.84 seconds wall clock time: 316 minutes 20.30 seconds (18980.30 seconds total)