Starting phenix.real_space_refine on Fri Sep 19 07:34:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bml_44702/09_2025/9bml_44702.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bml_44702/09_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_44702/09_2025/9bml_44702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bml_44702/09_2025/9bml_44702.map" model { file = "/net/cci-nas-00/data/ceres_data/9bml_44702/09_2025/9bml_44702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bml_44702/09_2025/9bml_44702.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.48, per 1000 atoms: 0.23 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: 1.61 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.31 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: 7.86 Time building geometry restraints manager: 2.28 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.410 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (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 ARG 0.008 0.000 ARG A2113 TYR 0.026 0.001 TYR A1546 PHE 0.023 0.001 PHE A2949 TRP 0.020 0.001 TRP A4592 HIS 0.003 0.000 HIS A3535 Details of bonding type rmsd covalent geometry : bond 0.00307 (24213) covalent geometry : angle 0.57251 (32838) hydrogen bonds : bond 0.13983 ( 1446) hydrogen bonds : angle 5.49657 ( 4194) *********************** 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 : 0.856 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 3478 LEU cc_start: 0.7915 (tp) cc_final: 0.7432 (pp) REVERT: A 3479 LEU cc_start: 0.8713 (tp) cc_final: 0.8338 (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: 0.1626 time to fit residues: 65.4386 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 : 0.777 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 A3233 ASN ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.128080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094580 restraints weight = 37689.627| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.56 r_work: 0.3042 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24213 Z= 0.219 Angle : 0.573 9.538 32838 Z= 0.288 Chirality : 0.042 0.203 3692 Planarity : 0.004 0.053 4206 Dihedral : 6.734 115.711 3268 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.23 % Allowed : 11.48 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.16), residues: 2929 helix: 2.17 (0.12), residues: 1718 sheet: -0.78 (0.34), residues: 230 loop : 0.49 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1543 TYR 0.019 0.002 TYR A2496 PHE 0.015 0.002 PHE A2900 TRP 0.016 0.001 TRP A2234 HIS 0.004 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00522 (24213) covalent geometry : angle 0.57341 (32838) hydrogen bonds : bond 0.04723 ( 1446) hydrogen bonds : angle 4.32465 ( 4194) *********************** 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 308 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1526 LYS cc_start: 0.5403 (pttp) cc_final: 0.4748 (mtpt) REVERT: A 1621 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7699 (mtt90) REVERT: A 1709 MET cc_start: 0.9172 (ttp) cc_final: 0.8521 (ptm) REVERT: A 1814 GLU cc_start: 0.8212 (tp30) cc_final: 0.7862 (tp30) REVERT: A 2205 GLU cc_start: 0.8496 (tp30) cc_final: 0.8281 (tp30) REVERT: A 2312 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8827 (p) REVERT: A 2326 THR cc_start: 0.9107 (m) cc_final: 0.8722 (p) REVERT: A 2373 MET cc_start: 0.8991 (mtm) cc_final: 0.8753 (mtm) REVERT: A 2461 MET cc_start: 0.8941 (mtp) cc_final: 0.8722 (mtp) REVERT: A 2901 TYR cc_start: 0.8497 (m-10) cc_final: 0.7842 (m-10) REVERT: A 2975 ASP cc_start: 0.8865 (m-30) cc_final: 0.8521 (m-30) REVERT: A 3016 GLU cc_start: 0.7765 (pp20) cc_final: 0.7421 (pp20) REVERT: A 3479 LEU cc_start: 0.8746 (tp) cc_final: 0.8412 (pp) REVERT: A 3785 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: A 4194 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8935 (mp) REVERT: A 4413 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.4241 (t80) REVERT: A 4429 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7670 (tt0) REVERT: A 4454 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7509 (mm-30) outliers start: 58 outliers final: 27 residues processed: 295 average time/residue: 0.1467 time to fit residues: 68.3059 Evaluate side-chains 255 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 1931 ASN 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 2365 SER 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 2618 VAL Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3158 ASN Chi-restraints excluded: chain A residue 3503 ILE 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 3789 ILE Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4274 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 44 optimal weight: 3.9990 chunk 154 optimal weight: 0.0370 chunk 59 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 238 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 202 optimal weight: 0.0470 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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** A4446 ASN 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 = 0.131516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097606 restraints weight = 37411.846| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.61 r_work: 0.3090 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1142 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= 0.103 Angle : 0.480 10.311 32838 Z= 0.240 Chirality : 0.038 0.146 3692 Planarity : 0.004 0.049 4206 Dihedral : 6.277 109.042 3265 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.46 % Allowed : 12.67 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.16), residues: 2929 helix: 2.39 (0.12), residues: 1720 sheet: -0.84 (0.33), residues: 236 loop : 0.57 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3164 TYR 0.024 0.001 TYR A1546 PHE 0.022 0.001 PHE A2949 TRP 0.016 0.001 TRP A2234 HIS 0.003 0.000 HIS A3535 Details of bonding type rmsd covalent geometry : bond 0.00219 (24213) covalent geometry : angle 0.47950 (32838) hydrogen bonds : bond 0.03861 ( 1446) hydrogen bonds : angle 3.99805 ( 4194) *********************** 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 288 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8366 (t0) cc_final: 0.7979 (t0) REVERT: A 1574 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8626 (mm-30) REVERT: A 1621 ARG cc_start: 0.7970 (mtt90) cc_final: 0.7409 (mtt90) REVERT: A 1635 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7745 (mt-10) REVERT: A 1709 MET cc_start: 0.9161 (ttp) cc_final: 0.8786 (ttp) REVERT: A 1814 GLU cc_start: 0.8066 (tp30) cc_final: 0.7502 (tp30) REVERT: A 2312 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8892 (p) REVERT: A 2632 LEU cc_start: 0.8704 (mt) cc_final: 0.8437 (mt) REVERT: A 2763 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7279 (ttp80) REVERT: A 2901 TYR cc_start: 0.8306 (m-10) cc_final: 0.7704 (m-10) REVERT: A 2975 ASP cc_start: 0.8834 (m-30) cc_final: 0.8512 (m-30) REVERT: A 3016 GLU cc_start: 0.7818 (pp20) cc_final: 0.7410 (pp20) REVERT: A 3479 LEU cc_start: 0.8724 (tp) cc_final: 0.8375 (pp) REVERT: A 3785 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: A 4311 LEU cc_start: 0.9033 (mt) cc_final: 0.8762 (mp) REVERT: A 4413 PHE cc_start: 0.5692 (OUTLIER) cc_final: 0.4259 (t80) REVERT: A 4429 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7493 (tt0) REVERT: A 4433 ASP cc_start: 0.7831 (m-30) cc_final: 0.7358 (m-30) REVERT: A 4454 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7512 (mm-30) outliers start: 38 outliers final: 17 residues processed: 276 average time/residue: 0.1562 time to fit residues: 67.3412 Evaluate side-chains 243 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2418 ASP Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2671 MET 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 3524 MET 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 4298 ASP Chi-restraints excluded: chain A residue 4315 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 252 optimal weight: 2.9990 chunk 87 optimal weight: 0.0770 chunk 158 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 283 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.129075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095215 restraints weight = 37528.480| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.59 r_work: 0.3059 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1365 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= 0.146 Angle : 0.503 10.010 32838 Z= 0.248 Chirality : 0.040 0.151 3692 Planarity : 0.004 0.051 4206 Dihedral : 6.085 108.164 3263 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.96 % Allowed : 13.47 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.16), residues: 2929 helix: 2.43 (0.12), residues: 1722 sheet: -0.93 (0.32), residues: 240 loop : 0.60 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A4263 TYR 0.029 0.001 TYR A4636 PHE 0.015 0.001 PHE A2949 TRP 0.015 0.001 TRP A2234 HIS 0.003 0.001 HIS A1817 Details of bonding type rmsd covalent geometry : bond 0.00343 (24213) covalent geometry : angle 0.50256 (32838) hydrogen bonds : bond 0.03904 ( 1446) hydrogen bonds : angle 3.96350 ( 4194) *********************** 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 297 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8346 (t0) cc_final: 0.7433 (t0) REVERT: A 1574 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8636 (mm-30) REVERT: A 1621 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7479 (mtt90) REVERT: A 1635 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 1655 LYS cc_start: 0.8498 (ptpp) cc_final: 0.7782 (pttt) REVERT: A 1688 THR cc_start: 0.8229 (m) cc_final: 0.7855 (p) REVERT: A 1709 MET cc_start: 0.9185 (ttp) cc_final: 0.8441 (ptm) REVERT: A 1814 GLU cc_start: 0.8126 (tp30) cc_final: 0.7554 (tp30) REVERT: A 1873 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8841 (mp) REVERT: A 2312 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8894 (p) REVERT: A 2763 ARG cc_start: 0.8079 (mtm110) cc_final: 0.7286 (ttp80) REVERT: A 2901 TYR cc_start: 0.8441 (m-10) cc_final: 0.7722 (m-10) REVERT: A 2975 ASP cc_start: 0.8859 (m-30) cc_final: 0.8520 (m-30) REVERT: A 3016 GLU cc_start: 0.7907 (pp20) cc_final: 0.7537 (pp20) REVERT: A 3479 LEU cc_start: 0.8727 (tp) cc_final: 0.8365 (pp) REVERT: A 3785 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: A 4194 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8838 (mp) REVERT: A 4311 LEU cc_start: 0.9060 (mt) cc_final: 0.8787 (mp) REVERT: A 4413 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.4568 (t80) REVERT: A 4419 MET cc_start: 0.7916 (mtp) cc_final: 0.7651 (mtp) REVERT: A 4429 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7581 (tt0) REVERT: A 4433 ASP cc_start: 0.7875 (m-30) cc_final: 0.7382 (m-30) REVERT: A 4454 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7577 (mm-30) outliers start: 51 outliers final: 27 residues processed: 284 average time/residue: 0.1538 time to fit residues: 68.7736 Evaluate side-chains 255 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 2140 SER Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2418 ASP Chi-restraints excluded: chain A residue 2450 THR 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 2990 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 285 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 chunk 234 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.130723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097483 restraints weight = 37078.056| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.56 r_work: 0.3086 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1514 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= 0.107 Angle : 0.476 10.078 32838 Z= 0.236 Chirality : 0.039 0.174 3692 Planarity : 0.004 0.050 4206 Dihedral : 5.836 103.998 3263 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.65 % Allowed : 14.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.16), residues: 2929 helix: 2.53 (0.12), residues: 1724 sheet: -0.93 (0.33), residues: 240 loop : 0.63 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1543 TYR 0.040 0.001 TYR A4636 PHE 0.016 0.001 PHE A2949 TRP 0.016 0.001 TRP A2234 HIS 0.002 0.000 HIS A3535 Details of bonding type rmsd covalent geometry : bond 0.00238 (24213) covalent geometry : angle 0.47615 (32838) hydrogen bonds : bond 0.03609 ( 1446) hydrogen bonds : angle 3.83827 ( 4194) *********************** 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 291 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8390 (t0) cc_final: 0.8138 (t0) REVERT: A 1574 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8625 (mm-30) REVERT: A 1620 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6543 (tm-30) REVERT: A 1621 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7523 (mtt90) REVERT: A 1655 LYS cc_start: 0.8486 (ptpp) cc_final: 0.7764 (pttt) REVERT: A 1688 THR cc_start: 0.8258 (m) cc_final: 0.7909 (p) REVERT: A 1709 MET cc_start: 0.9148 (ttp) cc_final: 0.8437 (ptm) REVERT: A 1873 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8836 (mp) REVERT: A 2308 ASP cc_start: 0.9093 (p0) cc_final: 0.8776 (p0) REVERT: A 2312 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8886 (p) REVERT: A 2632 LEU cc_start: 0.8699 (mt) cc_final: 0.8429 (mt) REVERT: A 2643 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7909 (mmm160) REVERT: A 2763 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7234 (ttp80) REVERT: A 2901 TYR cc_start: 0.8397 (m-10) cc_final: 0.7662 (m-10) REVERT: A 2975 ASP cc_start: 0.8753 (m-30) cc_final: 0.8430 (m-30) REVERT: A 3016 GLU cc_start: 0.7871 (pp20) cc_final: 0.7519 (pp20) REVERT: A 3479 LEU cc_start: 0.8654 (tp) cc_final: 0.8293 (pp) REVERT: A 3487 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8121 (mm-30) REVERT: A 3491 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7563 (mmtm) REVERT: A 4311 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8756 (mp) REVERT: A 4413 PHE cc_start: 0.6097 (OUTLIER) cc_final: 0.4543 (t80) REVERT: A 4419 MET cc_start: 0.8046 (mtp) cc_final: 0.7768 (mtp) REVERT: A 4429 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7550 (tt0) REVERT: A 4433 ASP cc_start: 0.7801 (m-30) cc_final: 0.7291 (m-30) REVERT: A 4454 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 4636 TYR cc_start: 0.8380 (m-80) cc_final: 0.7996 (m-80) outliers start: 43 outliers final: 25 residues processed: 277 average time/residue: 0.1591 time to fit residues: 69.2036 Evaluate side-chains 262 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 2312 VAL Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR 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 3205 LEU Chi-restraints excluded: chain A residue 3476 THR Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 4011 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 157 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 chunk 229 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1598 GLN ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3523 GLN A3837 HIS ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.089778 restraints weight = 38237.985| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.57 r_work: 0.2967 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 24213 Z= 0.322 Angle : 0.662 9.828 32838 Z= 0.330 Chirality : 0.045 0.191 3692 Planarity : 0.005 0.054 4206 Dihedral : 6.239 111.779 3263 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.50 % Allowed : 13.74 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.16), residues: 2929 helix: 2.08 (0.12), residues: 1719 sheet: -1.18 (0.32), residues: 241 loop : 0.39 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A4263 TYR 0.029 0.002 TYR A4636 PHE 0.021 0.002 PHE A2900 TRP 0.017 0.002 TRP A4222 HIS 0.008 0.002 HIS A3837 Details of bonding type rmsd covalent geometry : bond 0.00784 (24213) covalent geometry : angle 0.66221 (32838) hydrogen bonds : bond 0.04914 ( 1446) hydrogen bonds : angle 4.27393 ( 4194) *********************** 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 300 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8411 (t0) cc_final: 0.8138 (t0) REVERT: A 1620 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6883 (tm-30) REVERT: A 1621 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7629 (mtt90) REVERT: A 1652 LYS cc_start: 0.8503 (pttt) cc_final: 0.8190 (ptmm) REVERT: A 1688 THR cc_start: 0.8157 (m) cc_final: 0.7888 (p) REVERT: A 1709 MET cc_start: 0.9186 (ttp) cc_final: 0.8853 (ttp) REVERT: A 2063 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: A 2205 GLU cc_start: 0.8480 (tp30) cc_final: 0.8134 (tp30) REVERT: A 2232 MET cc_start: 0.9209 (mmt) cc_final: 0.8949 (mmp) REVERT: A 2430 ASN cc_start: 0.8742 (t0) cc_final: 0.8443 (t0) REVERT: A 2554 GLN cc_start: 0.8504 (mp10) cc_final: 0.8274 (mp10) REVERT: A 2975 ASP cc_start: 0.8911 (m-30) cc_final: 0.8504 (m-30) REVERT: A 3016 GLU cc_start: 0.7982 (pp20) cc_final: 0.7643 (pp20) REVERT: A 3479 LEU cc_start: 0.8692 (tp) cc_final: 0.8319 (pp) REVERT: A 3487 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8155 (mm-30) REVERT: A 3491 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7768 (mmtm) REVERT: A 4194 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9051 (mp) REVERT: A 4311 LEU cc_start: 0.9151 (mt) cc_final: 0.8914 (mp) REVERT: A 4413 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.5586 (t80) REVERT: A 4429 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7715 (tt0) REVERT: A 4433 ASP cc_start: 0.7950 (m-30) cc_final: 0.7415 (m-30) REVERT: A 4454 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 4595 GLN cc_start: 0.6640 (mt0) cc_final: 0.6427 (tp-100) outliers start: 65 outliers final: 48 residues processed: 285 average time/residue: 0.1574 time to fit residues: 70.2937 Evaluate side-chains 268 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 2002 LEU Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2140 SER Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2259 ILE Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2450 THR 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 2574 THR 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 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 3644 VAL Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3789 ILE Chi-restraints excluded: chain A residue 3833 LEU Chi-restraints excluded: chain A residue 3959 ILE 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 4380 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 235 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 291 optimal weight: 0.9990 chunk 292 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** A2314 ASN A2475 ASN A2491 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.127553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094728 restraints weight = 37290.748| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.54 r_work: 0.3046 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24213 Z= 0.116 Angle : 0.501 10.924 32838 Z= 0.248 Chirality : 0.039 0.157 3692 Planarity : 0.004 0.050 4206 Dihedral : 5.889 108.595 3263 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.46 % Allowed : 14.78 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.16), residues: 2929 helix: 2.39 (0.12), residues: 1721 sheet: -1.16 (0.32), residues: 240 loop : 0.53 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2292 TYR 0.028 0.001 TYR A4636 PHE 0.015 0.001 PHE A2682 TRP 0.019 0.001 TRP A2234 HIS 0.003 0.001 HIS A2463 Details of bonding type rmsd covalent geometry : bond 0.00259 (24213) covalent geometry : angle 0.50074 (32838) hydrogen bonds : bond 0.03844 ( 1446) hydrogen bonds : angle 3.91248 ( 4194) *********************** 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 281 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8406 (t0) cc_final: 0.8117 (t0) REVERT: A 1546 TYR cc_start: 0.7731 (p90) cc_final: 0.7518 (p90) REVERT: A 1620 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6809 (tm-30) REVERT: A 1621 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7676 (mtt90) REVERT: A 1639 GLU cc_start: 0.7575 (tp30) cc_final: 0.7020 (tp30) REVERT: A 1652 LYS cc_start: 0.8467 (pttt) cc_final: 0.8150 (ptmm) REVERT: A 1688 THR cc_start: 0.8183 (m) cc_final: 0.7886 (p) REVERT: A 1709 MET cc_start: 0.9131 (ttp) cc_final: 0.8796 (ttp) REVERT: A 1959 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8012 (mm-30) REVERT: A 2063 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: A 2145 MET cc_start: 0.8803 (mmt) cc_final: 0.7939 (mtp) REVERT: A 2308 ASP cc_start: 0.9168 (p0) cc_final: 0.8788 (p0) REVERT: A 2312 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8792 (p) REVERT: A 2430 ASN cc_start: 0.8706 (t0) cc_final: 0.8408 (t0) REVERT: A 2461 MET cc_start: 0.8841 (mtp) cc_final: 0.8439 (mtp) REVERT: A 2763 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7207 (ttp80) REVERT: A 2901 TYR cc_start: 0.8441 (m-10) cc_final: 0.7630 (m-10) REVERT: A 2975 ASP cc_start: 0.8808 (m-30) cc_final: 0.8453 (m-30) REVERT: A 3016 GLU cc_start: 0.7872 (pp20) cc_final: 0.7500 (pp20) REVERT: A 3479 LEU cc_start: 0.8667 (tp) cc_final: 0.8236 (pp) REVERT: A 3487 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 3491 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7771 (mmtm) REVERT: A 4311 LEU cc_start: 0.9085 (mt) cc_final: 0.8829 (mp) REVERT: A 4413 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.5402 (t80) REVERT: A 4429 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7836 (tt0) REVERT: A 4433 ASP cc_start: 0.7990 (m-30) cc_final: 0.7440 (m-30) REVERT: A 4454 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7423 (mm-30) outliers start: 38 outliers final: 29 residues processed: 273 average time/residue: 0.1514 time to fit residues: 65.2383 Evaluate side-chains 258 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 1692 ILE Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2108 ILE 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 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 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 3833 LEU 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 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 4 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 117 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.128288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095470 restraints weight = 37412.664| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.54 r_work: 0.3059 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24213 Z= 0.114 Angle : 0.497 10.874 32838 Z= 0.244 Chirality : 0.039 0.164 3692 Planarity : 0.004 0.050 4206 Dihedral : 5.689 104.398 3263 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.73 % Allowed : 14.63 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.16), residues: 2929 helix: 2.47 (0.12), residues: 1723 sheet: -1.15 (0.32), residues: 240 loop : 0.59 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2113 TYR 0.025 0.001 TYR A4636 PHE 0.015 0.001 PHE A2479 TRP 0.017 0.001 TRP A2234 HIS 0.002 0.000 HIS A3535 Details of bonding type rmsd covalent geometry : bond 0.00255 (24213) covalent geometry : angle 0.49654 (32838) hydrogen bonds : bond 0.03698 ( 1446) hydrogen bonds : angle 3.83596 ( 4194) *********************** 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 286 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8492 (t0) cc_final: 0.8129 (t0) REVERT: A 1546 TYR cc_start: 0.7749 (p90) cc_final: 0.7496 (p90) REVERT: A 1620 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6817 (tm-30) REVERT: A 1621 ARG cc_start: 0.8359 (mtt90) cc_final: 0.7797 (mtt90) REVERT: A 1639 GLU cc_start: 0.7431 (tp30) cc_final: 0.6805 (tp30) REVERT: A 1652 LYS cc_start: 0.8481 (pttt) cc_final: 0.8151 (ptmm) REVERT: A 1688 THR cc_start: 0.8201 (m) cc_final: 0.7912 (p) REVERT: A 1709 MET cc_start: 0.9114 (ttp) cc_final: 0.8778 (ttp) REVERT: A 1724 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7875 (p) REVERT: A 1873 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8849 (mp) REVERT: A 1959 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7994 (mm-30) REVERT: A 2308 ASP cc_start: 0.9072 (p0) cc_final: 0.8702 (p0) REVERT: A 2312 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8809 (p) REVERT: A 2414 GLN cc_start: 0.8735 (tp40) cc_final: 0.8279 (tp-100) REVERT: A 2430 ASN cc_start: 0.8755 (t0) cc_final: 0.8468 (t0) REVERT: A 2438 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8035 (pp20) REVERT: A 2461 MET cc_start: 0.8791 (mtp) cc_final: 0.8393 (mtp) REVERT: A 2763 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7179 (ttp80) REVERT: A 2901 TYR cc_start: 0.8396 (m-10) cc_final: 0.7626 (m-10) REVERT: A 2975 ASP cc_start: 0.8757 (m-30) cc_final: 0.8412 (m-30) REVERT: A 3016 GLU cc_start: 0.7876 (pp20) cc_final: 0.7519 (pp20) REVERT: A 3479 LEU cc_start: 0.8624 (tp) cc_final: 0.8280 (pp) REVERT: A 3487 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 3491 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7846 (mmtm) REVERT: A 4311 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8861 (mp) REVERT: A 4413 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.5311 (t80) REVERT: A 4429 GLN cc_start: 0.8540 (tp-100) cc_final: 0.7848 (tt0) REVERT: A 4433 ASP cc_start: 0.7959 (m-30) cc_final: 0.7409 (m-30) REVERT: A 4454 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7398 (mm-30) REVERT: A 4595 GLN cc_start: 0.6678 (mt0) cc_final: 0.6412 (tp-100) outliers start: 45 outliers final: 34 residues processed: 278 average time/residue: 0.1660 time to fit residues: 72.5967 Evaluate side-chains 265 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 1692 ILE 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 2108 ILE Chi-restraints excluded: chain A residue 2204 VAL 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 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 4011 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 292 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 290 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 284 optimal weight: 0.0170 chunk 259 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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** A1755 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.129639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097066 restraints weight = 37436.892| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.54 r_work: 0.3077 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2116 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= 0.101 Angle : 0.487 10.906 32838 Z= 0.239 Chirality : 0.039 0.164 3692 Planarity : 0.004 0.050 4206 Dihedral : 5.564 100.450 3263 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.73 % Allowed : 14.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.16), residues: 2929 helix: 2.54 (0.12), residues: 1723 sheet: -1.12 (0.32), residues: 241 loop : 0.62 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2113 TYR 0.026 0.001 TYR A4636 PHE 0.015 0.001 PHE A2949 TRP 0.016 0.001 TRP A1701 HIS 0.003 0.000 HIS A3535 Details of bonding type rmsd covalent geometry : bond 0.00218 (24213) covalent geometry : angle 0.48685 (32838) hydrogen bonds : bond 0.03524 ( 1446) hydrogen bonds : angle 3.77282 ( 4194) *********************** 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 289 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8451 (t0) cc_final: 0.8053 (t0) REVERT: A 1620 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6838 (tm-30) REVERT: A 1621 ARG cc_start: 0.8337 (mtt90) cc_final: 0.7496 (mtp-110) REVERT: A 1639 GLU cc_start: 0.7425 (tp30) cc_final: 0.6792 (tp30) REVERT: A 1652 LYS cc_start: 0.8482 (pttt) cc_final: 0.8129 (ptmm) REVERT: A 1688 THR cc_start: 0.8271 (m) cc_final: 0.8011 (p) REVERT: A 1873 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8778 (mp) REVERT: A 1959 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 2308 ASP cc_start: 0.9004 (p0) cc_final: 0.8628 (p0) REVERT: A 2312 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8869 (p) REVERT: A 2414 GLN cc_start: 0.8769 (tp40) cc_final: 0.8269 (tp-100) REVERT: A 2430 ASN cc_start: 0.8730 (t0) cc_final: 0.8475 (t0) REVERT: A 2438 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8016 (pp20) REVERT: A 2461 MET cc_start: 0.8770 (mtp) cc_final: 0.8394 (mtp) REVERT: A 2502 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8576 (mt) REVERT: A 2505 ASP cc_start: 0.9074 (p0) cc_final: 0.8811 (p0) REVERT: A 2632 LEU cc_start: 0.8702 (mt) cc_final: 0.8406 (mt) REVERT: A 2763 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7146 (ttp80) REVERT: A 2901 TYR cc_start: 0.8393 (m-10) cc_final: 0.7653 (m-10) REVERT: A 2975 ASP cc_start: 0.8758 (m-30) cc_final: 0.8466 (m-30) REVERT: A 2995 ASP cc_start: 0.8377 (t0) cc_final: 0.8171 (t0) REVERT: A 3016 GLU cc_start: 0.7831 (pp20) cc_final: 0.7463 (pp20) REVERT: A 3479 LEU cc_start: 0.8555 (tp) cc_final: 0.8217 (pp) REVERT: A 3487 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 3488 ARG cc_start: 0.7486 (ttp-170) cc_final: 0.7180 (ttp80) REVERT: A 3491 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7813 (mmtm) REVERT: A 3885 MET cc_start: 0.9180 (tpp) cc_final: 0.8811 (mmt) REVERT: A 4311 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8845 (mp) REVERT: A 4413 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.5508 (t80) REVERT: A 4429 GLN cc_start: 0.8537 (tp-100) cc_final: 0.7857 (tt0) REVERT: A 4433 ASP cc_start: 0.7910 (m-30) cc_final: 0.7433 (m-30) REVERT: A 4454 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7363 (mm-30) outliers start: 45 outliers final: 27 residues processed: 280 average time/residue: 0.1596 time to fit residues: 70.5257 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 : 0.859 ------------------------------------------------------------------------------- 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 1692 ILE 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 2204 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2371 THR 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 2996 GLU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3476 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 277 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 269 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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** A4063 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.128732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095929 restraints weight = 37562.985| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.55 r_work: 0.3058 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24213 Z= 0.116 Angle : 0.502 11.011 32838 Z= 0.245 Chirality : 0.039 0.169 3692 Planarity : 0.004 0.051 4206 Dihedral : 5.522 98.985 3263 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.34 % Allowed : 15.24 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.16), residues: 2929 helix: 2.55 (0.12), residues: 1724 sheet: -1.11 (0.32), residues: 240 loop : 0.63 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2113 TYR 0.026 0.001 TYR A4636 PHE 0.016 0.001 PHE A2479 TRP 0.016 0.001 TRP A2234 HIS 0.002 0.000 HIS A3837 Details of bonding type rmsd covalent geometry : bond 0.00266 (24213) covalent geometry : angle 0.50206 (32838) hydrogen bonds : bond 0.03565 ( 1446) hydrogen bonds : angle 3.77742 ( 4194) ********************** 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 275 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 ASP cc_start: 0.8442 (t0) cc_final: 0.7978 (t0) REVERT: A 1620 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6847 (tm-30) REVERT: A 1621 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7496 (mtp-110) REVERT: A 1639 GLU cc_start: 0.7356 (tp30) cc_final: 0.6723 (tp30) REVERT: A 1652 LYS cc_start: 0.8508 (pttt) cc_final: 0.8179 (ptmm) REVERT: A 1688 THR cc_start: 0.8225 (m) cc_final: 0.7975 (p) REVERT: A 1724 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7784 (p) REVERT: A 1873 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8845 (mp) REVERT: A 2273 ARG cc_start: 0.8150 (mmt180) cc_final: 0.7845 (mmt180) REVERT: A 2308 ASP cc_start: 0.9015 (p0) cc_final: 0.8624 (p0) REVERT: A 2312 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 2430 ASN cc_start: 0.8780 (t0) cc_final: 0.8500 (t0) REVERT: A 2438 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8020 (pp20) REVERT: A 2461 MET cc_start: 0.8824 (mtp) cc_final: 0.8461 (mtp) REVERT: A 2502 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 2632 LEU cc_start: 0.8704 (mt) cc_final: 0.8420 (mt) REVERT: A 2763 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7156 (ttp80) REVERT: A 2975 ASP cc_start: 0.8772 (m-30) cc_final: 0.8421 (m-30) REVERT: A 2995 ASP cc_start: 0.8415 (t0) cc_final: 0.8158 (t0) REVERT: A 3016 GLU cc_start: 0.7873 (pp20) cc_final: 0.7499 (pp20) REVERT: A 3479 LEU cc_start: 0.8545 (tp) cc_final: 0.8204 (pp) REVERT: A 3487 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 3488 ARG cc_start: 0.7544 (ttp-170) cc_final: 0.7148 (ttp80) REVERT: A 3491 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7708 (mmtm) REVERT: A 3885 MET cc_start: 0.9167 (tpp) cc_final: 0.8783 (mmt) REVERT: A 4311 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 4413 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.5469 (t80) REVERT: A 4429 GLN cc_start: 0.8544 (tp-100) cc_final: 0.7870 (tt0) REVERT: A 4433 ASP cc_start: 0.8024 (m-30) cc_final: 0.7559 (m-30) REVERT: A 4454 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 4595 GLN cc_start: 0.6667 (mt0) cc_final: 0.6385 (tp-100) outliers start: 35 outliers final: 27 residues processed: 266 average time/residue: 0.1563 time to fit residues: 64.5148 Evaluate side-chains 266 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 1692 ILE Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2002 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 2075 LEU Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2371 THR 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 3154 LEU Chi-restraints excluded: chain A residue 3476 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 159 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 38 optimal weight: 0.0070 chunk 275 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 overall best weight: 2.1404 ------------------------------------------------------------------------------- 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** A4156 ASN A4191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093374 restraints weight = 38040.371| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.61 r_work: 0.3010 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24213 Z= 0.196 Angle : 0.561 11.533 32838 Z= 0.276 Chirality : 0.041 0.193 3692 Planarity : 0.004 0.052 4206 Dihedral : 5.677 103.385 3263 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.57 % Allowed : 15.20 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.16), residues: 2929 helix: 2.41 (0.12), residues: 1722 sheet: -1.19 (0.32), residues: 242 loop : 0.53 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2113 TYR 0.024 0.001 TYR A4636 PHE 0.016 0.002 PHE A2343 TRP 0.017 0.001 TRP A2234 HIS 0.004 0.001 HIS A1817 Details of bonding type rmsd covalent geometry : bond 0.00470 (24213) covalent geometry : angle 0.56091 (32838) hydrogen bonds : bond 0.04093 ( 1446) hydrogen bonds : angle 3.95177 ( 4194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4475.46 seconds wall clock time: 77 minutes 33.01 seconds (4653.01 seconds total)