Starting phenix.real_space_refine on Fri Jun 20 23:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bml_44702/06_2025/9bml_44702.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bml_44702/06_2025/9bml_44702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bml_44702/06_2025/9bml_44702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bml_44702/06_2025/9bml_44702.map" model { file = "/net/cci-nas-00/data/ceres_data/9bml_44702/06_2025/9bml_44702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bml_44702/06_2025/9bml_44702.cif" } resolution = 3.3 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= 0.058 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 1 5.21 5 S 117 5.16 5 C 15068 2.51 5 N 4090 2.21 5 O 4421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23706 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 23593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2937, 23593 Classifications: {'peptide': 2937} Link IDs: {'PTRANS': 131, 'TRANS': 2805} Chain breaks: 3 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 13.93, per 1000 atoms: 0.59 Number of scatterers: 23706 At special positions: 0 Unit cell: (145.824, 195.3, 148.428, 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 117 16.00 P 9 15.00 Mg 1 11.99 O 4421 8.00 N 4090 7.00 C 15068 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: 6.46 Conformation dependent library (CDL) restraints added in 3.1 seconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 20 sheets defined 64.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 1457 through 1473 Processing helix chain 'A' and resid 1489 through 1510 removed outlier: 3.540A pdb=" N SER A1510 " --> pdb=" O ALA A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1515 removed outlier: 3.601A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.821A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A1538 " --> pdb=" O PHE A1534 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A1550 " --> pdb=" O TYR A1546 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.102A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1613 Processing helix chain 'A' and resid 1615 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1654 removed outlier: 3.872A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A1654 " --> pdb=" O GLN A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 4.344A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1770 through 1772 No H-bonds generated for 'chain 'A' and resid 1770 through 1772' Processing helix chain 'A' and resid 1777 through 1797 Processing helix chain 'A' and resid 1801 through 1828 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1912 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: 3.851A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A1987 " --> pdb=" O ARG A1983 " (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 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2255 through 2259 removed outlier: 3.872A 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 2279 through 2290 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.839A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A2297 " --> pdb=" O GLU A2294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2293 through 2297' Processing helix chain 'A' and resid 2308 through 2313 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2359 removed outlier: 3.571A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A2359 " --> pdb=" O THR A2355 " (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 2431 through 2441 Processing helix chain 'A' and resid 2450 through 2476 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 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.834A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2610 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.235A 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 2756 Processing helix chain 'A' and resid 2757 through 2758 No H-bonds generated for 'chain 'A' and resid 2757 through 2758' Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 4.540A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.856A 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 removed outlier: 3.599A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 removed outlier: 3.564A pdb=" N ALA A2866 " --> pdb=" O ASP A2862 " (cutoff:3.500A) 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: 4.100A 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 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.541A pdb=" N LYS A3076 " --> pdb=" O SER A3072 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3086 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3241 removed outlier: 3.731A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3495 removed outlier: 4.981A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3517 removed outlier: 4.987A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.512A 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 Processing helix chain 'A' and resid 3605 through 3608 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3638 through 3641 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3756 Processing helix chain 'A' and resid 3759 through 3762 Processing helix chain 'A' and resid 3763 through 3817 removed outlier: 4.158A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN A3800 " --> pdb=" O THR A3796 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3818 through 3821 Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.668A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.639A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 Processing helix chain 'A' and resid 3876 through 3894 removed outlier: 4.492A pdb=" N ILE A3881 " --> pdb=" O HIS A3877 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR A3882 " --> pdb=" O GLN A3878 " (cutoff:3.500A) Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3917 through 3921 removed outlier: 3.786A pdb=" N THR A3921 " --> pdb=" O ALA A3918 " (cutoff:3.500A) Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.246A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.715A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.251A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4015 through 4023 removed outlier: 4.455A pdb=" N MET A4018 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A4019 " --> pdb=" O SER A4016 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE A4020 " --> pdb=" O PHE A4017 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A4023 " --> pdb=" O ILE A4020 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.684A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.077A 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: 3.719A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (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: 3.614A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4194 removed outlier: 3.509A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 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 4328 through 4346 removed outlier: 3.563A pdb=" N MET A4346 " --> pdb=" O LYS A4342 " (cutoff:3.500A) Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.190A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 removed outlier: 3.974A pdb=" N ARG A4415 " --> pdb=" O ARG A4411 " (cutoff:3.500A) Processing helix chain 'A' and resid 4445 through 4457 Processing helix chain 'A' and resid 4474 through 4498 Processing helix chain 'A' and resid 4500 through 4507 removed outlier: 3.524A pdb=" N LEU A4504 " --> pdb=" O GLY A4500 " (cutoff:3.500A) 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 1476 through 1479 removed outlier: 4.254A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 3.519A pdb=" N GLY A1675 " --> pdb=" O ILE A1665 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.808A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.570A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1929 removed outlier: 6.314A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2000 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2253 removed outlier: 6.789A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.042A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 6.806A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.642A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.157A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 Processing sheet with id=AB7, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.566A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.745A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4508 through 4510 removed outlier: 3.551A pdb=" N VAL A4593 " --> pdb=" O CYS A4540 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.213A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A4609 " --> pdb=" O ILE A4619 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR A4621 " --> pdb=" O LEU A4607 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU A4607 " --> pdb=" O THR A4621 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASP A4623 " --> pdb=" O VAL A4605 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL A4605 " --> pdb=" O ASP A4623 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1446 hydrogen bonds defined for protein. 4194 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: 14.83 Time building geometry restraints manager: 7.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6684 1.33 - 1.46: 4047 1.46 - 1.58: 13272 1.58 - 1.70: 14 1.70 - 1.82: 196 Bond restraints: 24213 Sorted by residual: 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 2.96e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N LEU A2526 " pdb=" CA LEU A2526 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.11e-02 8.12e+03 9.80e+00 bond pdb=" N ILE A2521 " pdb=" CA ILE A2521 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.17e+00 bond pdb=" N ILE A4626 " pdb=" CA ILE A4626 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.30e-02 5.92e+03 8.12e+00 ... (remaining 24208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 32481 2.33 - 4.66: 306 4.66 - 6.99: 35 6.99 - 9.32: 11 9.32 - 11.65: 5 Bond angle restraints: 32838 Sorted by residual: angle pdb=" C THR A4628 " pdb=" CA THR A4628 " pdb=" CB THR A4628 " ideal model delta sigma weight residual 116.54 110.71 5.83 1.15e+00 7.56e-01 2.57e+01 angle pdb=" N THR A2523 " pdb=" CA THR A2523 " pdb=" C THR A2523 " ideal model delta sigma weight residual 113.97 108.85 5.12 1.28e+00 6.10e-01 1.60e+01 angle pdb=" C1' ADP A4701 " pdb=" C2' ADP A4701 " pdb=" C3' ADP A4701 " ideal model delta sigma weight residual 111.00 100.23 10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N PRO A4632 " pdb=" CA PRO A4632 " pdb=" C PRO A4632 " ideal model delta sigma weight residual 113.53 108.66 4.87 1.39e+00 5.18e-01 1.23e+01 angle pdb=" PA ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " ideal model delta sigma weight residual 120.50 130.97 -10.47 3.00e+00 1.11e-01 1.22e+01 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.73: 13534 23.73 - 47.45: 980 47.45 - 71.18: 154 71.18 - 94.91: 22 94.91 - 118.63: 3 Dihedral angle restraints: 14693 sinusoidal: 6090 harmonic: 8603 Sorted by residual: dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.63 118.63 1 2.00e+01 2.50e-03 3.55e+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 -60.00 -172.39 112.39 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 46.69 -106.70 1 2.00e+01 2.50e-03 3.09e+01 ... (remaining 14690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2983 0.047 - 0.094: 542 0.094 - 0.141: 156 0.141 - 0.188: 7 0.188 - 0.235: 4 Chirality restraints: 3692 Sorted by residual: chirality pdb=" CB ILE A4492 " pdb=" CA ILE A4492 " pdb=" CG1 ILE A4492 " pdb=" CG2 ILE A4492 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU A3770 " pdb=" CB LEU A3770 " pdb=" CD1 LEU A3770 " pdb=" CD2 LEU A3770 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE A1997 " pdb=" N ILE A1997 " pdb=" C ILE A1997 " pdb=" CB ILE A1997 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 3689 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A4633 " 0.519 9.50e-02 1.11e+02 2.33e-01 3.32e+01 pdb=" NE ARG A4633 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A4633 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A4633 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A4633 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A3978 " -0.059 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A3979 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A3979 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A3979 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2410 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.74e+00 pdb=" N PRO A2411 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A2411 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A2411 " 0.039 5.00e-02 4.00e+02 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 128 2.54 - 3.13: 18100 3.13 - 3.72: 38104 3.72 - 4.31: 51883 4.31 - 4.90: 88925 Nonbonded interactions: 197140 Sorted by model distance: nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4705 " model vdw 1.949 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4705 " model vdw 1.975 2.170 nonbonded pdb=" OE1 GLU A3487 " pdb=" NZ LYS A3491 " model vdw 2.224 3.120 nonbonded pdb=" OG SER A2623 " pdb=" OE1 GLU A3006 " model vdw 2.235 3.040 nonbonded pdb=" OE2 GLU A2205 " pdb=" NE2 GLN A2209 " model vdw 2.242 3.120 ... (remaining 197135 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 63.860 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.003 0.109 24213 Z= 0.164 Angle : 0.573 11.652 32838 Z= 0.305 Chirality : 0.040 0.235 3692 Planarity : 0.005 0.233 4206 Dihedral : 16.059 118.632 9105 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.37 % Favored : 98.60 % Rotamer: Outliers : 0.38 % Allowed : 12.63 % Favored : 86.99 % 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: 2.14 (0.16), residues: 2929 helix: 2.27 (0.12), residues: 1713 sheet: -0.48 (0.35), residues: 223 loop : 0.47 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4592 HIS 0.003 0.000 HIS A3535 PHE 0.023 0.001 PHE A2949 TYR 0.026 0.001 TYR A1546 ARG 0.008 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.13983 ( 1446) hydrogen bonds : angle 5.49657 ( 4194) covalent geometry : bond 0.00307 (24213) covalent geometry : angle 0.57251 (32838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 257 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1814 GLU cc_start: 0.8107 (tp30) cc_final: 0.7681 (tp30) REVERT: A 2043 LYS cc_start: 0.9068 (mttm) cc_final: 0.8654 (mtmm) REVERT: A 2975 ASP cc_start: 0.8797 (m-30) cc_final: 0.8102 (m-30) REVERT: A 3479 LEU cc_start: 0.8713 (tp) cc_final: 0.8433 (pp) REVERT: A 4270 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 4453 ASN cc_start: 0.7991 (t0) cc_final: 0.7784 (t0) outliers start: 10 outliers final: 3 residues processed: 260 average time/residue: 0.3943 time to fit residues: 159.9191 Evaluate side-chains 242 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 4492 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 229 optimal weight: 8.9990 chunk 88 optimal weight: 0.1980 chunk 139 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 266 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A3233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097366 restraints weight = 36997.804| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.51 r_work: 0.3116 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24213 Z= 0.121 Angle : 0.505 7.270 32838 Z= 0.253 Chirality : 0.039 0.215 3692 Planarity : 0.004 0.051 4206 Dihedral : 6.555 116.413 3268 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.65 % Allowed : 11.13 % Favored : 87.22 % 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: 2.26 (0.16), residues: 2929 helix: 2.38 (0.12), residues: 1719 sheet: -0.67 (0.34), residues: 237 loop : 0.58 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1701 HIS 0.002 0.001 HIS A3907 PHE 0.017 0.001 PHE A2949 TYR 0.016 0.001 TYR A2748 ARG 0.005 0.000 ARG A4633 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 1446) hydrogen bonds : angle 4.18555 ( 4194) covalent geometry : bond 0.00268 (24213) covalent geometry : angle 0.50458 (32838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 262 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1579 MET cc_start: 0.7943 (mmm) cc_final: 0.7542 (mmm) REVERT: A 1621 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7646 (mtt90) REVERT: A 1635 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 1709 MET cc_start: 0.9122 (ttp) cc_final: 0.8477 (ptm) REVERT: A 1814 GLU cc_start: 0.8075 (tp30) cc_final: 0.7664 (tp30) REVERT: A 1941 MET cc_start: 0.8982 (mmm) cc_final: 0.8149 (mmt) REVERT: A 2205 GLU cc_start: 0.8409 (tp30) cc_final: 0.8200 (tp30) REVERT: A 2222 MET cc_start: 0.8624 (mtm) cc_final: 0.8220 (mtt) REVERT: A 2312 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8776 (p) REVERT: A 2461 MET cc_start: 0.8652 (mtp) cc_final: 0.8423 (mtp) REVERT: A 2632 LEU cc_start: 0.8688 (mt) cc_final: 0.8429 (mt) REVERT: A 2901 TYR cc_start: 0.8262 (m-10) cc_final: 0.7730 (m-10) REVERT: A 2975 ASP cc_start: 0.8824 (m-30) cc_final: 0.8508 (m-30) REVERT: A 3478 LEU cc_start: 0.8103 (tp) cc_final: 0.7560 (pp) REVERT: A 3479 LEU cc_start: 0.8743 (tp) cc_final: 0.8320 (pp) REVERT: A 3785 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: A 4454 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7334 (mp0) outliers start: 43 outliers final: 14 residues processed: 296 average time/residue: 0.3849 time to fit residues: 181.6289 Evaluate side-chains 240 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4492 ILE Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 281 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** A1856 GLN A1894 GLN A1973 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094736 restraints weight = 37453.590| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.58 r_work: 0.3050 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24213 Z= 0.174 Angle : 0.527 10.473 32838 Z= 0.261 Chirality : 0.041 0.147 3692 Planarity : 0.004 0.052 4206 Dihedral : 6.332 114.354 3263 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.88 % Allowed : 12.28 % Favored : 85.83 % 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: 2.20 (0.16), residues: 2929 helix: 2.34 (0.12), residues: 1724 sheet: -0.82 (0.33), residues: 229 loop : 0.53 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.004 0.001 HIS A2476 PHE 0.015 0.002 PHE A2949 TYR 0.023 0.001 TYR A1546 ARG 0.007 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 1446) hydrogen bonds : angle 4.07690 ( 4194) covalent geometry : bond 0.00415 (24213) covalent geometry : angle 0.52707 (32838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8345 (t0) cc_final: 0.7983 (t0) REVERT: A 1635 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 1688 THR cc_start: 0.8168 (m) cc_final: 0.7745 (p) REVERT: A 1709 MET cc_start: 0.9180 (ttp) cc_final: 0.8793 (ttp) REVERT: A 1814 GLU cc_start: 0.8135 (tp30) cc_final: 0.7602 (tp30) REVERT: A 2205 GLU cc_start: 0.8424 (tp30) cc_final: 0.8113 (tp30) REVERT: A 2373 MET cc_start: 0.9011 (mtm) cc_final: 0.8764 (mtm) REVERT: A 2481 MET cc_start: 0.8631 (ttm) cc_final: 0.8195 (ttm) REVERT: A 2901 TYR cc_start: 0.8435 (m-10) cc_final: 0.7728 (m-10) REVERT: A 2975 ASP cc_start: 0.8846 (m-30) cc_final: 0.8506 (m-30) REVERT: A 3016 GLU cc_start: 0.7783 (pp20) cc_final: 0.7433 (pp20) REVERT: A 3024 ASP cc_start: 0.8009 (t0) cc_final: 0.7765 (t0) REVERT: A 3479 LEU cc_start: 0.8762 (tp) cc_final: 0.8383 (pp) REVERT: A 3785 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 4194 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8894 (mp) REVERT: A 4311 LEU cc_start: 0.9074 (mt) cc_final: 0.8811 (mp) REVERT: A 4413 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.4860 (t80) REVERT: A 4433 ASP cc_start: 0.7919 (m-30) cc_final: 0.7472 (m-30) REVERT: A 4454 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7683 (mm-30) outliers start: 49 outliers final: 27 residues processed: 280 average time/residue: 0.3987 time to fit residues: 176.5193 Evaluate side-chains 248 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1590 ASP Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1931 ASN Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2365 SER Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2418 ASP Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3476 THR Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4413 PHE Chi-restraints excluded: chain A residue 4492 ILE Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 200 optimal weight: 0.0050 chunk 177 optimal weight: 7.9990 chunk 259 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 246 optimal weight: 0.4980 chunk 174 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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** A2475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.130928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097202 restraints weight = 37569.378| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.60 r_work: 0.3084 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24213 Z= 0.105 Angle : 0.485 10.219 32838 Z= 0.239 Chirality : 0.039 0.168 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.043 109.355 3263 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.50 % Allowed : 13.13 % Favored : 85.37 % 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: 2.32 (0.16), residues: 2929 helix: 2.46 (0.12), residues: 1723 sheet: -0.91 (0.32), residues: 250 loop : 0.62 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.002 0.000 HIS A3535 PHE 0.018 0.001 PHE A2949 TYR 0.023 0.001 TYR A1546 ARG 0.005 0.000 ARG A4263 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 1446) hydrogen bonds : angle 3.89669 ( 4194) covalent geometry : bond 0.00228 (24213) covalent geometry : angle 0.48488 (32838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 254 time to evaluate : 6.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1484 CYS cc_start: 0.7937 (t) cc_final: 0.6854 (t) REVERT: A 1539 ASP cc_start: 0.8226 (t0) cc_final: 0.7750 (t0) REVERT: A 1546 TYR cc_start: 0.7900 (p90) cc_final: 0.7658 (p90) REVERT: A 1635 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 1639 GLU cc_start: 0.7416 (tp30) cc_final: 0.6883 (tp30) REVERT: A 1688 THR cc_start: 0.8202 (m) cc_final: 0.7798 (p) REVERT: A 1709 MET cc_start: 0.9162 (ttp) cc_final: 0.8798 (ttp) REVERT: A 1814 GLU cc_start: 0.8070 (tp30) cc_final: 0.7484 (tp30) REVERT: A 1873 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8839 (mp) REVERT: A 2312 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 2481 MET cc_start: 0.8706 (ttm) cc_final: 0.8272 (ttm) REVERT: A 2632 LEU cc_start: 0.8699 (mt) cc_final: 0.8424 (mt) REVERT: A 2763 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7274 (ttp80) REVERT: A 2901 TYR cc_start: 0.8352 (m-10) cc_final: 0.7694 (m-10) REVERT: A 2975 ASP cc_start: 0.8848 (m-30) cc_final: 0.8510 (m-30) REVERT: A 3016 GLU cc_start: 0.7715 (pp20) cc_final: 0.7390 (pp20) REVERT: A 3479 LEU cc_start: 0.8690 (tp) cc_final: 0.8309 (pp) REVERT: A 3487 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8012 (mm-30) REVERT: A 3491 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7583 (mmtm) REVERT: A 3785 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: A 4311 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8763 (mp) REVERT: A 4413 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.4958 (t80) REVERT: A 4419 MET cc_start: 0.7656 (mtp) cc_final: 0.7319 (mtp) REVERT: A 4433 ASP cc_start: 0.7853 (m-30) cc_final: 0.7378 (m-30) REVERT: A 4454 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7574 (mm-30) outliers start: 39 outliers final: 21 residues processed: 281 average time/residue: 0.6867 time to fit residues: 313.2992 Evaluate side-chains 255 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1590 ASP Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2365 SER Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4298 ASP Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4413 PHE Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4492 ILE Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 159 optimal weight: 5.9990 chunk 169 optimal weight: 0.4980 chunk 182 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 275 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 249 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094545 restraints weight = 37659.211| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.60 r_work: 0.3048 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24213 Z= 0.166 Angle : 0.515 8.359 32838 Z= 0.254 Chirality : 0.040 0.154 3692 Planarity : 0.004 0.052 4206 Dihedral : 5.939 109.205 3263 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.84 % Allowed : 13.86 % Favored : 84.30 % 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: 2.29 (0.16), residues: 2929 helix: 2.44 (0.12), residues: 1722 sheet: -0.96 (0.32), residues: 248 loop : 0.62 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.003 0.001 HIS A2827 PHE 0.013 0.001 PHE A2912 TYR 0.033 0.001 TYR A4636 ARG 0.006 0.000 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 1446) hydrogen bonds : angle 3.94037 ( 4194) covalent geometry : bond 0.00397 (24213) covalent geometry : angle 0.51514 (32838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1484 CYS cc_start: 0.7752 (t) cc_final: 0.7307 (t) REVERT: A 1539 ASP cc_start: 0.8354 (t0) cc_final: 0.7862 (t0) REVERT: A 1546 TYR cc_start: 0.7927 (p90) cc_final: 0.7684 (p90) REVERT: A 1620 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6564 (tm-30) REVERT: A 1635 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7795 (mt-10) REVERT: A 1639 GLU cc_start: 0.7590 (tp30) cc_final: 0.7117 (tp30) REVERT: A 1655 LYS cc_start: 0.8519 (ptpp) cc_final: 0.7805 (pttt) REVERT: A 1688 THR cc_start: 0.8209 (m) cc_final: 0.7853 (p) REVERT: A 1709 MET cc_start: 0.9177 (ttp) cc_final: 0.8466 (ptm) REVERT: A 1814 GLU cc_start: 0.8120 (tp30) cc_final: 0.7513 (tp30) REVERT: A 1873 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8855 (mp) REVERT: A 2312 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8892 (p) REVERT: A 2481 MET cc_start: 0.8796 (ttm) cc_final: 0.8366 (ttm) REVERT: A 2554 GLN cc_start: 0.8472 (mp10) cc_final: 0.8257 (mp10) REVERT: A 2901 TYR cc_start: 0.8521 (m-10) cc_final: 0.7721 (m-10) REVERT: A 2975 ASP cc_start: 0.8818 (m-30) cc_final: 0.8478 (m-30) REVERT: A 3016 GLU cc_start: 0.7699 (pp20) cc_final: 0.7418 (pp20) REVERT: A 3024 ASP cc_start: 0.8203 (t70) cc_final: 0.7840 (t0) REVERT: A 3479 LEU cc_start: 0.8653 (tp) cc_final: 0.8305 (pp) REVERT: A 3487 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 3491 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7761 (mmtm) REVERT: A 4194 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8873 (mp) REVERT: A 4311 LEU cc_start: 0.9075 (mt) cc_final: 0.8804 (mp) REVERT: A 4413 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5243 (t80) REVERT: A 4419 MET cc_start: 0.8072 (mtp) cc_final: 0.7817 (mtp) REVERT: A 4433 ASP cc_start: 0.7820 (m-30) cc_final: 0.7284 (m-30) REVERT: A 4454 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7611 (mm-30) outliers start: 48 outliers final: 28 residues processed: 277 average time/residue: 0.3797 time to fit residues: 164.8727 Evaluate side-chains 261 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1590 ASP Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3476 THR Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4298 ASP Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4413 PHE Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4492 ILE Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 183 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 288 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** A2475 ASN A3837 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.129306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095989 restraints weight = 37444.776| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.56 r_work: 0.3062 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24213 Z= 0.128 Angle : 0.490 10.907 32838 Z= 0.242 Chirality : 0.039 0.156 3692 Planarity : 0.004 0.051 4206 Dihedral : 5.814 105.565 3263 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.00 % Allowed : 13.67 % Favored : 84.34 % 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: 2.33 (0.16), residues: 2929 helix: 2.48 (0.12), residues: 1722 sheet: -0.96 (0.33), residues: 240 loop : 0.60 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.008 0.001 HIS A3837 PHE 0.014 0.001 PHE A2949 TYR 0.037 0.001 TYR A4636 ARG 0.006 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 1446) hydrogen bonds : angle 3.86701 ( 4194) covalent geometry : bond 0.00295 (24213) covalent geometry : angle 0.49021 (32838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1484 CYS cc_start: 0.7729 (t) cc_final: 0.7194 (t) REVERT: A 1539 ASP cc_start: 0.8388 (t0) cc_final: 0.7851 (t0) REVERT: A 1546 TYR cc_start: 0.7885 (p90) cc_final: 0.7609 (p90) REVERT: A 1620 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6599 (tm-30) REVERT: A 1635 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 1639 GLU cc_start: 0.7574 (tp30) cc_final: 0.7025 (tp30) REVERT: A 1655 LYS cc_start: 0.8517 (ptpp) cc_final: 0.7795 (pttt) REVERT: A 1688 THR cc_start: 0.8231 (m) cc_final: 0.7889 (p) REVERT: A 1709 MET cc_start: 0.9150 (ttp) cc_final: 0.8793 (ttp) REVERT: A 1814 GLU cc_start: 0.8088 (tp30) cc_final: 0.7499 (tp30) REVERT: A 1873 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8897 (mp) REVERT: A 2063 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: A 2308 ASP cc_start: 0.9126 (p0) cc_final: 0.8799 (p0) REVERT: A 2312 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8898 (p) REVERT: A 2430 ASN cc_start: 0.8662 (t0) cc_final: 0.8364 (t0) REVERT: A 2461 MET cc_start: 0.8504 (mtp) cc_final: 0.8173 (mtp) REVERT: A 2481 MET cc_start: 0.8815 (ttm) cc_final: 0.8382 (ttm) REVERT: A 2509 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8197 (tttt) REVERT: A 2632 LEU cc_start: 0.8703 (mt) cc_final: 0.8407 (mt) REVERT: A 2763 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7189 (ttp80) REVERT: A 2901 TYR cc_start: 0.8482 (m-10) cc_final: 0.7684 (m-10) REVERT: A 2975 ASP cc_start: 0.8816 (m-30) cc_final: 0.8469 (m-30) REVERT: A 3016 GLU cc_start: 0.7792 (pp20) cc_final: 0.7440 (pp20) REVERT: A 3024 ASP cc_start: 0.8244 (t70) cc_final: 0.7880 (t0) REVERT: A 3479 LEU cc_start: 0.8623 (tp) cc_final: 0.8289 (pp) REVERT: A 3487 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 3491 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7825 (mmtm) REVERT: A 3496 PHE cc_start: 0.7700 (t80) cc_final: 0.6732 (t80) REVERT: A 4194 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8829 (mp) REVERT: A 4311 LEU cc_start: 0.9062 (mt) cc_final: 0.8789 (mp) REVERT: A 4413 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5225 (t80) REVERT: A 4433 ASP cc_start: 0.7850 (m-30) cc_final: 0.7316 (m-30) REVERT: A 4454 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7593 (mm-30) REVERT: A 4636 TYR cc_start: 0.8401 (m-80) cc_final: 0.8042 (m-80) outliers start: 52 outliers final: 34 residues processed: 281 average time/residue: 0.3862 time to fit residues: 171.5993 Evaluate side-chains 270 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1590 ASP Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2259 ILE Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3476 THR Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4298 ASP Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4413 PHE Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4492 ILE Chi-restraints excluded: chain A residue 4493 SER Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 247 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.129546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.096341 restraints weight = 37616.413| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.57 r_work: 0.3070 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24213 Z= 0.116 Angle : 0.481 8.127 32838 Z= 0.238 Chirality : 0.039 0.154 3692 Planarity : 0.004 0.051 4206 Dihedral : 5.655 102.255 3263 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.07 % Allowed : 13.82 % Favored : 84.11 % 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: 2.39 (0.16), residues: 2929 helix: 2.54 (0.12), residues: 1722 sheet: -0.99 (0.32), residues: 240 loop : 0.62 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.002 0.000 HIS A3837 PHE 0.012 0.001 PHE A3004 TYR 0.026 0.001 TYR A4636 ARG 0.006 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1446) hydrogen bonds : angle 3.81752 ( 4194) covalent geometry : bond 0.00262 (24213) covalent geometry : angle 0.48052 (32838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1484 CYS cc_start: 0.7636 (t) cc_final: 0.7126 (t) REVERT: A 1539 ASP cc_start: 0.8431 (t0) cc_final: 0.8015 (t0) REVERT: A 1546 TYR cc_start: 0.7795 (p90) cc_final: 0.7552 (p90) REVERT: A 1620 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6610 (tm-30) REVERT: A 1639 GLU cc_start: 0.7566 (tp30) cc_final: 0.7043 (tp30) REVERT: A 1688 THR cc_start: 0.8258 (m) cc_final: 0.7933 (p) REVERT: A 1814 GLU cc_start: 0.8095 (tp30) cc_final: 0.7481 (tp30) REVERT: A 1873 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8826 (mp) REVERT: A 2063 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: A 2308 ASP cc_start: 0.9044 (p0) cc_final: 0.8646 (p0) REVERT: A 2312 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8898 (p) REVERT: A 2418 ASP cc_start: 0.8506 (m-30) cc_final: 0.8303 (m-30) REVERT: A 2430 ASN cc_start: 0.8718 (t0) cc_final: 0.8440 (t0) REVERT: A 2461 MET cc_start: 0.8590 (mtp) cc_final: 0.8290 (mtp) REVERT: A 2481 MET cc_start: 0.8810 (ttm) cc_final: 0.8311 (ttm) REVERT: A 2505 ASP cc_start: 0.9087 (p0) cc_final: 0.8786 (p0) REVERT: A 2509 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8185 (tttt) REVERT: A 2632 LEU cc_start: 0.8696 (mt) cc_final: 0.8408 (mt) REVERT: A 2763 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7167 (ttp80) REVERT: A 2901 TYR cc_start: 0.8436 (m-10) cc_final: 0.7620 (m-10) REVERT: A 2975 ASP cc_start: 0.8814 (m-30) cc_final: 0.8467 (m-30) REVERT: A 3016 GLU cc_start: 0.7814 (pp20) cc_final: 0.7475 (pp20) REVERT: A 3479 LEU cc_start: 0.8657 (tp) cc_final: 0.8329 (pp) REVERT: A 3487 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 3491 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7840 (mmtm) REVERT: A 4194 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 4311 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8780 (mp) REVERT: A 4413 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.5239 (t80) REVERT: A 4419 MET cc_start: 0.8205 (mtp) cc_final: 0.7929 (mtp) REVERT: A 4433 ASP cc_start: 0.7880 (m-30) cc_final: 0.7357 (m-30) REVERT: A 4454 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7524 (mm-30) outliers start: 54 outliers final: 37 residues processed: 288 average time/residue: 0.3666 time to fit residues: 168.1048 Evaluate side-chains 269 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1590 ASP Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2259 ILE Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3476 THR Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4298 ASP Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4413 PHE Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4492 ILE Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 78 optimal weight: 0.7980 chunk 246 optimal weight: 0.8980 chunk 123 optimal weight: 0.3980 chunk 147 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 104 optimal weight: 0.0040 chunk 229 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.130959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097504 restraints weight = 37334.907| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.60 r_work: 0.3090 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24213 Z= 0.098 Angle : 0.477 10.327 32838 Z= 0.235 Chirality : 0.038 0.152 3692 Planarity : 0.004 0.050 4206 Dihedral : 5.507 99.392 3263 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.57 % Allowed : 14.55 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.48 (0.16), residues: 2929 helix: 2.61 (0.12), residues: 1722 sheet: -0.95 (0.33), residues: 243 loop : 0.67 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.003 0.000 HIS A3535 PHE 0.016 0.001 PHE A2949 TYR 0.060 0.001 TYR A4636 ARG 0.008 0.000 ARG A2113 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 1446) hydrogen bonds : angle 3.75031 ( 4194) covalent geometry : bond 0.00208 (24213) covalent geometry : angle 0.47732 (32838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1484 CYS cc_start: 0.7530 (t) cc_final: 0.6834 (t) REVERT: A 1539 ASP cc_start: 0.8316 (t0) cc_final: 0.7990 (t0) REVERT: A 1620 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6584 (tm-30) REVERT: A 1639 GLU cc_start: 0.7515 (tp30) cc_final: 0.6951 (tp30) REVERT: A 1688 THR cc_start: 0.8203 (m) cc_final: 0.7897 (p) REVERT: A 1724 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7838 (p) REVERT: A 1873 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8905 (mp) REVERT: A 2273 ARG cc_start: 0.7874 (mmt180) cc_final: 0.7409 (mmt180) REVERT: A 2308 ASP cc_start: 0.9000 (p0) cc_final: 0.8616 (p0) REVERT: A 2312 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 2418 ASP cc_start: 0.8433 (m-30) cc_final: 0.8223 (m-30) REVERT: A 2430 ASN cc_start: 0.8717 (t0) cc_final: 0.8443 (t0) REVERT: A 2438 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7955 (pp20) REVERT: A 2461 MET cc_start: 0.8343 (mtp) cc_final: 0.8092 (mtp) REVERT: A 2502 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8465 (mt) REVERT: A 2505 ASP cc_start: 0.9107 (p0) cc_final: 0.8746 (p0) REVERT: A 2509 LYS cc_start: 0.8311 (ttmt) cc_final: 0.8031 (tttt) REVERT: A 2632 LEU cc_start: 0.8692 (mt) cc_final: 0.8431 (mt) REVERT: A 2763 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7205 (ttp80) REVERT: A 2901 TYR cc_start: 0.8359 (m-10) cc_final: 0.7618 (m-10) REVERT: A 2975 ASP cc_start: 0.8757 (m-30) cc_final: 0.8471 (m-30) REVERT: A 3016 GLU cc_start: 0.7792 (pp20) cc_final: 0.7442 (pp20) REVERT: A 3479 LEU cc_start: 0.8637 (tp) cc_final: 0.8315 (pp) REVERT: A 3487 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7836 (mm-30) REVERT: A 3491 LYS cc_start: 0.8354 (mmtm) cc_final: 0.7975 (mmtm) REVERT: A 3885 MET cc_start: 0.9159 (tpp) cc_final: 0.8778 (mmt) REVERT: A 4183 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 4311 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8810 (mp) REVERT: A 4413 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.5188 (t80) REVERT: A 4419 MET cc_start: 0.8250 (mtp) cc_final: 0.8009 (mtp) REVERT: A 4433 ASP cc_start: 0.7851 (m-30) cc_final: 0.7401 (m-30) REVERT: A 4454 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 41 outliers final: 25 residues processed: 272 average time/residue: 0.3753 time to fit residues: 163.3870 Evaluate side-chains 257 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1590 ASP Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3476 THR Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4196 TYR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4413 PHE Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4492 ILE Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 285 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 273 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 258 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** A3837 HIS A4063 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097517 restraints weight = 37384.802| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.53 r_work: 0.3086 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24213 Z= 0.115 Angle : 0.492 8.685 32838 Z= 0.242 Chirality : 0.039 0.169 3692 Planarity : 0.004 0.059 4206 Dihedral : 5.475 97.966 3263 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.57 % Allowed : 14.70 % Favored : 83.72 % 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: 2.48 (0.16), residues: 2929 helix: 2.62 (0.12), residues: 1721 sheet: -0.98 (0.32), residues: 251 loop : 0.66 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A4592 HIS 0.006 0.001 HIS A3837 PHE 0.012 0.001 PHE A2949 TYR 0.049 0.001 TYR A4636 ARG 0.013 0.000 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 1446) hydrogen bonds : angle 3.75290 ( 4194) covalent geometry : bond 0.00262 (24213) covalent geometry : angle 0.49174 (32838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8365 (t0) cc_final: 0.8030 (t0) REVERT: A 1620 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6604 (tm-30) REVERT: A 1639 GLU cc_start: 0.7557 (tp30) cc_final: 0.6845 (tp30) REVERT: A 1688 THR cc_start: 0.8212 (m) cc_final: 0.7907 (p) REVERT: A 1724 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7800 (p) REVERT: A 1814 GLU cc_start: 0.8042 (tp30) cc_final: 0.7641 (tp30) REVERT: A 1873 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8839 (mp) REVERT: A 2273 ARG cc_start: 0.7898 (mmt180) cc_final: 0.7576 (mmt180) REVERT: A 2308 ASP cc_start: 0.9001 (p0) cc_final: 0.8599 (p0) REVERT: A 2312 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8902 (p) REVERT: A 2418 ASP cc_start: 0.8443 (m-30) cc_final: 0.8236 (m-30) REVERT: A 2430 ASN cc_start: 0.8734 (t0) cc_final: 0.8466 (t0) REVERT: A 2438 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7958 (pp20) REVERT: A 2461 MET cc_start: 0.8394 (mtp) cc_final: 0.8122 (mtp) REVERT: A 2481 MET cc_start: 0.8701 (ttm) cc_final: 0.8439 (ttm) REVERT: A 2502 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 2505 ASP cc_start: 0.9110 (p0) cc_final: 0.8746 (p0) REVERT: A 2509 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8050 (tttt) REVERT: A 2632 LEU cc_start: 0.8702 (mt) cc_final: 0.8420 (mt) REVERT: A 2763 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7244 (ttp80) REVERT: A 2901 TYR cc_start: 0.8428 (m-10) cc_final: 0.7666 (m-10) REVERT: A 2975 ASP cc_start: 0.8765 (m-30) cc_final: 0.8419 (m-30) REVERT: A 3016 GLU cc_start: 0.7846 (pp20) cc_final: 0.7510 (pp20) REVERT: A 3479 LEU cc_start: 0.8634 (tp) cc_final: 0.8314 (pp) REVERT: A 3491 LYS cc_start: 0.8359 (mmtm) cc_final: 0.7827 (tptp) REVERT: A 3745 LEU cc_start: 0.8031 (mt) cc_final: 0.7597 (tt) REVERT: A 3773 LEU cc_start: 0.7310 (mm) cc_final: 0.6983 (mp) REVERT: A 4311 LEU cc_start: 0.9100 (mt) cc_final: 0.8836 (mp) REVERT: A 4413 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.5254 (t80) REVERT: A 4433 ASP cc_start: 0.7910 (m-30) cc_final: 0.7400 (m-30) REVERT: A 4454 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7486 (mm-30) REVERT: A 4526 GLN cc_start: 0.6476 (tp40) cc_final: 0.6271 (tp40) outliers start: 41 outliers final: 33 residues processed: 268 average time/residue: 0.3877 time to fit residues: 164.7953 Evaluate side-chains 271 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1590 ASP Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3476 THR Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4413 PHE Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4492 ILE Chi-restraints excluded: chain A residue 4493 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 148 optimal weight: 0.7980 chunk 253 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 115 optimal weight: 0.0050 chunk 287 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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** A2491 GLN A3837 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097883 restraints weight = 37555.067| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.56 r_work: 0.3085 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24213 Z= 0.109 Angle : 0.494 10.133 32838 Z= 0.243 Chirality : 0.039 0.172 3692 Planarity : 0.004 0.051 4206 Dihedral : 5.429 97.797 3263 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.50 % Allowed : 14.93 % Favored : 83.57 % 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: 2.50 (0.16), residues: 2929 helix: 2.64 (0.12), residues: 1721 sheet: -0.94 (0.32), residues: 243 loop : 0.64 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.006 0.000 HIS A3837 PHE 0.013 0.001 PHE A2949 TYR 0.049 0.001 TYR A4636 ARG 0.010 0.000 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 1446) hydrogen bonds : angle 3.73130 ( 4194) covalent geometry : bond 0.00247 (24213) covalent geometry : angle 0.49419 (32838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8339 (t0) cc_final: 0.8000 (t0) REVERT: A 1620 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6596 (tm-30) REVERT: A 1639 GLU cc_start: 0.7511 (tp30) cc_final: 0.6843 (tp30) REVERT: A 1688 THR cc_start: 0.8225 (m) cc_final: 0.7930 (p) REVERT: A 1724 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7783 (p) REVERT: A 1814 GLU cc_start: 0.8081 (tp30) cc_final: 0.7667 (tp30) REVERT: A 1873 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8881 (mp) REVERT: A 2273 ARG cc_start: 0.8009 (mmt180) cc_final: 0.7691 (mmt180) REVERT: A 2308 ASP cc_start: 0.8986 (p0) cc_final: 0.8580 (p0) REVERT: A 2312 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8898 (p) REVERT: A 2418 ASP cc_start: 0.8449 (m-30) cc_final: 0.8243 (m-30) REVERT: A 2430 ASN cc_start: 0.8741 (t0) cc_final: 0.8480 (t0) REVERT: A 2438 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7959 (pp20) REVERT: A 2461 MET cc_start: 0.8360 (mtp) cc_final: 0.8109 (mtp) REVERT: A 2481 MET cc_start: 0.8688 (ttm) cc_final: 0.8387 (ttm) REVERT: A 2502 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8477 (mt) REVERT: A 2505 ASP cc_start: 0.9072 (p0) cc_final: 0.8788 (p0) REVERT: A 2509 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8044 (tttt) REVERT: A 2632 LEU cc_start: 0.8691 (mt) cc_final: 0.8412 (mt) REVERT: A 2763 ARG cc_start: 0.8038 (mtm110) cc_final: 0.7234 (ttp80) REVERT: A 2901 TYR cc_start: 0.8412 (m-10) cc_final: 0.7669 (m-10) REVERT: A 2975 ASP cc_start: 0.8767 (m-30) cc_final: 0.8422 (m-30) REVERT: A 3016 GLU cc_start: 0.7842 (pp20) cc_final: 0.7494 (pp20) REVERT: A 3479 LEU cc_start: 0.8621 (tp) cc_final: 0.8302 (pp) REVERT: A 3488 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7196 (ttp80) REVERT: A 3885 MET cc_start: 0.9128 (tpp) cc_final: 0.8749 (mmt) REVERT: A 4049 TYR cc_start: 0.7427 (m-80) cc_final: 0.7036 (t80) REVERT: A 4311 LEU cc_start: 0.9098 (mt) cc_final: 0.8835 (mp) REVERT: A 4413 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.5246 (t80) REVERT: A 4433 ASP cc_start: 0.7978 (m-30) cc_final: 0.7475 (m-30) REVERT: A 4454 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7477 (mm-30) outliers start: 39 outliers final: 33 residues processed: 270 average time/residue: 0.4035 time to fit residues: 172.6573 Evaluate side-chains 270 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1508 LYS Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1590 ASP Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3476 THR Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4413 PHE Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4492 ILE Chi-restraints excluded: chain A residue 4493 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 20 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 74 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.0050 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 291 optimal weight: 6.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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** A3837 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098715 restraints weight = 37316.419| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.54 r_work: 0.3100 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24213 Z= 0.100 Angle : 0.489 9.674 32838 Z= 0.241 Chirality : 0.038 0.163 3692 Planarity : 0.004 0.050 4206 Dihedral : 5.358 96.142 3263 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.57 % Allowed : 15.05 % Favored : 83.38 % 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: 2929 helix: 2.67 (0.12), residues: 1721 sheet: -0.88 (0.33), residues: 243 loop : 0.65 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.006 0.000 HIS A3837 PHE 0.013 0.001 PHE A2949 TYR 0.048 0.001 TYR A4636 ARG 0.011 0.000 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 1446) hydrogen bonds : angle 3.70534 ( 4194) covalent geometry : bond 0.00218 (24213) covalent geometry : angle 0.48917 (32838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11048.10 seconds wall clock time: 194 minutes 3.47 seconds (11643.47 seconds total)