Starting phenix.real_space_refine on Fri Sep 19 03:07:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0u_47371/09_2025/9e0u_47371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0u_47371/09_2025/9e0u_47371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e0u_47371/09_2025/9e0u_47371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0u_47371/09_2025/9e0u_47371.map" model { file = "/net/cci-nas-00/data/ceres_data/9e0u_47371/09_2025/9e0u_47371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0u_47371/09_2025/9e0u_47371.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 108 5.16 5 C 14031 2.51 5 N 3817 2.21 5 O 4084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22051 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2783, 21937 Classifications: {'peptide': 2783} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 3, 'PTRANS': 125, 'TRANS': 2654} Chain breaks: 13 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 25, 'ASN:plan1': 5, 'TYR:plan': 5, 'ARG:plan': 10, 'ASP:plan': 12, 'GLN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 299 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.36, per 1000 atoms: 0.24 Number of scatterers: 22051 At special positions: 0 Unit cell: (117.81, 142.12, 205.7, 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 108 16.00 P 9 15.00 Mg 2 11.99 O 4084 8.00 N 3817 7.00 C 14031 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: 1.92 Conformation dependent library (CDL) restraints added in 959.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 22 sheets defined 61.7% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 3.733A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1584 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1631 removed outlier: 3.655A pdb=" N TYR A1630 " --> pdb=" O PRO A1627 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1627 through 1631' Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.652A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1730 removed outlier: 4.235A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.844A 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 1768 Processing helix chain 'A' and resid 1776 through 1798 removed outlier: 4.126A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1828 removed outlier: 3.610A pdb=" N SER A1828 " --> pdb=" O SER A1824 " (cutoff:3.500A) 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 1950 Processing helix chain 'A' and resid 1964 through 1986 removed outlier: 3.814A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.779A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2113 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.486A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2311 through 2316 removed outlier: 3.622A pdb=" N ASN A2316 " --> pdb=" O GLU A2313 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2365 through 2369 removed outlier: 3.780A pdb=" N LEU A2369 " --> pdb=" O GLU A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2384 Processing helix chain 'A' and resid 2410 through 2428 Proline residue: A2425 - end of helix removed outlier: 3.727A pdb=" N THR A2428 " --> pdb=" O GLN A2424 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2443 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.961A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 4.263A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) 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 2548 through 2552 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 4.135A 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 2628 through 2638 Processing helix chain 'A' and resid 2677 through 2690 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 5.044A pdb=" N GLN A2746 " --> pdb=" O ALA A2742 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2762 through 2764 No H-bonds generated for 'chain 'A' and resid 2762 through 2764' Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.983A pdb=" N GLU A2775 " --> pdb=" O ALA A2771 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A2776 " --> pdb=" O ALA A2772 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A2777 " --> pdb=" O MET A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.952A 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: 3.567A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 4.370A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A2903 " --> pdb=" O VAL A2899 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.716A pdb=" N GLN A2928 " --> pdb=" O ARG A2924 " (cutoff:3.500A) 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: 3.668A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3022 through 3041 Processing helix chain 'A' and resid 3047 through 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.816A pdb=" N LYS A3076 " --> pdb=" O SER A3072 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3240 removed outlier: 3.783A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3451 through 3502 removed outlier: 4.439A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A3488 " --> pdb=" O ALA A3484 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS A3491 " --> pdb=" O GLU A3487 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN A3498 " --> pdb=" O GLU A3494 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 removed outlier: 3.750A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.783A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3616 through 3618 No H-bonds generated for 'chain 'A' and resid 3616 through 3618' Processing helix chain 'A' and resid 3619 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.655A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 3.766A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A3696 " --> pdb=" O LEU A3692 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3755 Processing helix chain 'A' and resid 3759 through 3762 Processing helix chain 'A' and resid 3763 through 3818 removed outlier: 3.824A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL A3784 " --> pdb=" O VAL A3780 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU A3785 " --> pdb=" O THR A3781 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A3786 " --> pdb=" O ARG A3782 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.677A pdb=" N TYR A3841 " --> pdb=" O HIS A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.799A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 removed outlier: 4.012A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (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 4018 through 4023 removed outlier: 3.541A pdb=" N MET A4021 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A4022 " --> pdb=" O SER A4019 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.796A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.845A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4090 Processing helix chain 'A' and resid 4098 through 4101 removed outlier: 3.979A pdb=" N LEU A4101 " --> pdb=" O ASN A4098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4098 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.697A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 Processing helix chain 'A' and resid 4175 through 4193 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.604A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.906A pdb=" N PHE A4278 " --> pdb=" O THR A4274 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 removed outlier: 4.099A pdb=" N LEU A4321 " --> pdb=" O THR A4317 " (cutoff:3.500A) Processing helix chain 'A' and resid 4328 through 4349 removed outlier: 3.841A pdb=" N LEU A4349 " --> pdb=" O LYS A4345 " (cutoff:3.500A) Processing helix chain 'A' and resid 4380 through 4391 Processing helix chain 'A' and resid 4392 through 4395 Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4497 removed outlier: 3.836A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) Processing helix chain 'A' and resid 4512 through 4514 No H-bonds generated for 'chain 'A' and resid 4512 through 4514' Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 3.640A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A1675 " --> pdb=" O ILE A1665 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.723A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.474A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1928 Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2000 Processing sheet with id=AA6, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 6.637A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.515A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 4.200A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB4, first strand: chain 'A' and resid 2935 through 2936 Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.158A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3587 through 3590 Processing sheet with id=AB7, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 5.952A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB9, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 3.582A pdb=" N MET A4095 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.682A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4508 through 4510 removed outlier: 6.572A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 4568 through 4571 Processing sheet with id=AC4, first strand: chain 'A' and resid 4618 through 4625 removed outlier: 4.069A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) 1299 hydrogen bonds defined for protein. 3825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7245 1.34 - 1.46: 4206 1.46 - 1.58: 10865 1.58 - 1.70: 11 1.70 - 1.82: 180 Bond restraints: 22507 Sorted by residual: bond pdb=" CA ILE A4391 " pdb=" C ILE A4391 " ideal model delta sigma weight residual 1.520 1.533 -0.013 8.80e-03 1.29e+04 2.14e+00 bond pdb=" CD1 TYR A3836 " pdb=" CE1 TYR A3836 " ideal model delta sigma weight residual 1.382 1.339 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" C4 ADP A4804 " pdb=" C5 ADP A4804 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C4 ADP A4805 " pdb=" C5 ADP A4805 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C LEU A2668 " pdb=" N PRO A2669 " ideal model delta sigma weight residual 1.331 1.346 -0.015 1.27e-02 6.20e+03 1.47e+00 ... (remaining 22502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 29850 1.95 - 3.91: 596 3.91 - 5.86: 87 5.86 - 7.82: 24 7.82 - 9.77: 4 Bond angle restraints: 30561 Sorted by residual: angle pdb=" C ILE A4391 " pdb=" CA ILE A4391 " pdb=" CB ILE A4391 " ideal model delta sigma weight residual 114.35 109.53 4.82 1.06e+00 8.90e-01 2.07e+01 angle pdb=" C LEU A2813 " pdb=" N GLU A2814 " pdb=" CA GLU A2814 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" N GLU A3575 " pdb=" CA GLU A3575 " pdb=" CB GLU A3575 " ideal model delta sigma weight residual 110.39 115.76 -5.37 1.66e+00 3.63e-01 1.05e+01 angle pdb=" N GLN A4079 " pdb=" CA GLN A4079 " pdb=" CB GLN A4079 " ideal model delta sigma weight residual 110.28 114.94 -4.66 1.55e+00 4.16e-01 9.03e+00 angle pdb=" CA ILE A2385 " pdb=" CB ILE A2385 " pdb=" CG2 ILE A2385 " ideal model delta sigma weight residual 110.50 115.60 -5.10 1.70e+00 3.46e-01 9.00e+00 ... (remaining 30556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 12597 22.64 - 45.28: 933 45.28 - 67.91: 75 67.91 - 90.55: 29 90.55 - 113.19: 2 Dihedral angle restraints: 13636 sinusoidal: 5492 harmonic: 8144 Sorted by residual: dihedral pdb=" O1B ADP A4805 " pdb=" O3A ADP A4805 " pdb=" PB ADP A4805 " pdb=" PA ADP A4805 " ideal model delta sinusoidal sigma weight residual -60.00 -173.19 113.19 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" C5' ADP A4805 " pdb=" O5' ADP A4805 " pdb=" PA ADP A4805 " pdb=" O2A ADP A4805 " ideal model delta sinusoidal sigma weight residual -60.00 -169.66 109.66 1 2.00e+01 2.50e-03 3.21e+01 dihedral pdb=" C5' ADP A4804 " pdb=" O5' ADP A4804 " pdb=" PA ADP A4804 " pdb=" O2A ADP A4804 " ideal model delta sinusoidal sigma weight residual -60.00 -143.20 83.20 1 2.00e+01 2.50e-03 2.12e+01 ... (remaining 13633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2626 0.048 - 0.095: 690 0.095 - 0.143: 168 0.143 - 0.190: 11 0.190 - 0.238: 4 Chirality restraints: 3499 Sorted by residual: chirality pdb=" CB ILE A2385 " pdb=" CA ILE A2385 " pdb=" CG1 ILE A2385 " pdb=" CG2 ILE A2385 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL A2146 " pdb=" CA VAL A2146 " pdb=" CG1 VAL A2146 " pdb=" CG2 VAL A2146 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL A3638 " pdb=" CA VAL A3638 " pdb=" CG1 VAL A3638 " pdb=" CG2 VAL A3638 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3496 not shown) Planarity restraints: 3905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A2668 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO A2669 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A2669 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A2669 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A4268 " -0.015 2.00e-02 2.50e+03 1.57e-02 4.31e+00 pdb=" CG PHE A4268 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A4268 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A4268 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A4268 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A4268 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A4268 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1882 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO A1883 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1883 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1883 " -0.027 5.00e-02 4.00e+02 ... (remaining 3902 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 148 2.54 - 3.13: 16597 3.13 - 3.72: 35901 3.72 - 4.31: 45660 4.31 - 4.90: 77903 Nonbonded interactions: 176209 Sorted by model distance: nonbonded pdb=" O2B ADP A4801 " pdb="MG MG A4806 " model vdw 1.953 2.170 nonbonded pdb=" O1G ATP A4802 " pdb="MG MG A4803 " model vdw 1.973 2.170 nonbonded pdb=" OG SER A2231 " pdb=" OE2 GLU A2344 " model vdw 1.973 3.040 nonbonded pdb=" O2B ATP A4802 " pdb="MG MG A4803 " model vdw 2.007 2.170 nonbonded pdb=" OD2 ASP A1958 " pdb="MG MG A4806 " model vdw 2.017 2.170 ... (remaining 176204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.670 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22507 Z= 0.190 Angle : 0.673 9.769 30561 Z= 0.338 Chirality : 0.045 0.238 3499 Planarity : 0.005 0.061 3905 Dihedral : 14.958 113.187 8332 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.16), residues: 2755 helix: 1.21 (0.13), residues: 1595 sheet: 0.23 (0.35), residues: 227 loop : -0.77 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3782 TYR 0.017 0.002 TYR A3836 PHE 0.035 0.002 PHE A4268 TRP 0.017 0.001 TRP A1701 HIS 0.010 0.001 HIS A3151 Details of bonding type rmsd covalent geometry : bond 0.00442 (22507) covalent geometry : angle 0.67311 (30561) hydrogen bonds : bond 0.09350 ( 1299) hydrogen bonds : angle 5.10187 ( 3825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 1655 LYS cc_start: 0.8006 (mppt) cc_final: 0.7788 (mttt) REVERT: A 1967 MET cc_start: 0.8427 (mmm) cc_final: 0.8116 (mmm) REVERT: A 2012 MET cc_start: 0.8456 (mmm) cc_final: 0.8193 (tpt) REVERT: A 2361 MET cc_start: 0.8784 (mmp) cc_final: 0.8456 (mmt) REVERT: A 2479 PHE cc_start: 0.8265 (m-80) cc_final: 0.8037 (m-10) REVERT: A 2500 TRP cc_start: 0.8669 (m100) cc_final: 0.8368 (m100) REVERT: A 2560 HIS cc_start: 0.8586 (t-90) cc_final: 0.8380 (t-90) REVERT: A 2621 ASN cc_start: 0.8544 (m110) cc_final: 0.8134 (m110) REVERT: A 2633 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8541 (mmmt) REVERT: A 2905 LEU cc_start: 0.8374 (mt) cc_final: 0.8018 (pp) REVERT: A 3014 ASN cc_start: 0.7775 (m-40) cc_final: 0.6845 (m-40) REVERT: A 3022 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7744 (mm-30) REVERT: A 3195 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8446 (mt-10) REVERT: A 3196 GLU cc_start: 0.7719 (pp20) cc_final: 0.7369 (pp20) REVERT: A 3199 MET cc_start: 0.8458 (ttt) cc_final: 0.8046 (tmm) REVERT: A 3489 TRP cc_start: 0.7539 (m-10) cc_final: 0.7319 (m-10) REVERT: A 3494 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6988 (tt0) REVERT: A 3610 THR cc_start: 0.8300 (p) cc_final: 0.8039 (p) REVERT: A 3747 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8488 (tppt) REVERT: A 3805 SER cc_start: 0.8789 (m) cc_final: 0.8559 (t) REVERT: A 4343 MET cc_start: 0.8899 (mmm) cc_final: 0.8699 (mmm) REVERT: A 4387 TRP cc_start: 0.7251 (t60) cc_final: 0.7039 (t60) REVERT: A 4469 VAL cc_start: 0.7960 (t) cc_final: 0.7707 (m) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1529 time to fit residues: 63.6600 Evaluate side-chains 193 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2314 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.107457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.084542 restraints weight = 58307.134| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.57 r_work: 0.3289 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22507 Z= 0.170 Angle : 0.577 8.010 30561 Z= 0.288 Chirality : 0.041 0.169 3499 Planarity : 0.004 0.051 3905 Dihedral : 6.244 118.156 3068 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.93 % Allowed : 8.69 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.16), residues: 2755 helix: 1.71 (0.13), residues: 1601 sheet: 0.40 (0.34), residues: 240 loop : -0.73 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A3782 TYR 0.014 0.001 TYR A2193 PHE 0.014 0.001 PHE A3823 TRP 0.018 0.001 TRP A1701 HIS 0.006 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00394 (22507) covalent geometry : angle 0.57713 (30561) hydrogen bonds : bond 0.03648 ( 1299) hydrogen bonds : angle 4.24690 ( 3825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 2012 MET cc_start: 0.8586 (mmm) cc_final: 0.8320 (tpt) REVERT: A 2361 MET cc_start: 0.8761 (mmp) cc_final: 0.8547 (mmt) REVERT: A 2479 PHE cc_start: 0.8315 (m-80) cc_final: 0.8056 (m-10) REVERT: A 2500 TRP cc_start: 0.8612 (m100) cc_final: 0.8286 (m100) REVERT: A 2560 HIS cc_start: 0.8638 (t-90) cc_final: 0.8412 (t-90) REVERT: A 2905 LEU cc_start: 0.8381 (mt) cc_final: 0.7874 (pp) REVERT: A 3193 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7731 (mm-30) REVERT: A 3195 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8431 (mt-10) REVERT: A 3199 MET cc_start: 0.8494 (ttt) cc_final: 0.8017 (tmm) REVERT: A 3489 TRP cc_start: 0.7688 (m-10) cc_final: 0.7432 (m-10) REVERT: A 3610 THR cc_start: 0.8357 (p) cc_final: 0.8060 (p) REVERT: A 3747 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8473 (tppt) REVERT: A 3805 SER cc_start: 0.8807 (m) cc_final: 0.8598 (t) REVERT: A 4081 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8661 (t0) REVERT: A 4387 TRP cc_start: 0.7296 (t60) cc_final: 0.6974 (t60) REVERT: A 4469 VAL cc_start: 0.7901 (t) cc_final: 0.7593 (m) outliers start: 22 outliers final: 16 residues processed: 216 average time/residue: 0.1519 time to fit residues: 54.0767 Evaluate side-chains 205 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4214 SER Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4453 ASN Chi-restraints excluded: chain A residue 4488 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 207 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1855 GLN A1867 ASN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2960 GLN A4156 ASN ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4566 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.107553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.084639 restraints weight = 58227.973| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.52 r_work: 0.3292 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22507 Z= 0.136 Angle : 0.547 8.860 30561 Z= 0.271 Chirality : 0.040 0.167 3499 Planarity : 0.004 0.062 3905 Dihedral : 6.047 117.425 3068 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.56 % Allowed : 11.01 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.16), residues: 2755 helix: 1.93 (0.13), residues: 1599 sheet: 0.43 (0.34), residues: 240 loop : -0.63 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A3782 TYR 0.022 0.001 TYR A3836 PHE 0.022 0.001 PHE A3823 TRP 0.016 0.001 TRP A1701 HIS 0.004 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00312 (22507) covalent geometry : angle 0.54722 (30561) hydrogen bonds : bond 0.03418 ( 1299) hydrogen bonds : angle 4.06365 ( 3825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1656 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7574 (tttm) REVERT: A 1814 GLU cc_start: 0.8758 (tp30) cc_final: 0.8326 (tp30) REVERT: A 1861 MET cc_start: 0.8375 (ttt) cc_final: 0.8116 (ttt) REVERT: A 2012 MET cc_start: 0.8622 (mmm) cc_final: 0.8360 (tpt) REVERT: A 2262 ASP cc_start: 0.8709 (t0) cc_final: 0.8507 (t0) REVERT: A 2361 MET cc_start: 0.8783 (mmp) cc_final: 0.8565 (mmt) REVERT: A 2479 PHE cc_start: 0.8283 (m-80) cc_final: 0.8034 (m-10) REVERT: A 2500 TRP cc_start: 0.8620 (m100) cc_final: 0.8268 (m100) REVERT: A 2560 HIS cc_start: 0.8714 (t-90) cc_final: 0.8484 (t-90) REVERT: A 2813 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8884 (tt) REVERT: A 2867 MET cc_start: 0.8093 (mmm) cc_final: 0.7807 (mmm) REVERT: A 2905 LEU cc_start: 0.8327 (mt) cc_final: 0.7897 (pp) REVERT: A 2994 MET cc_start: 0.8568 (ppp) cc_final: 0.8320 (ptm) REVERT: A 3014 ASN cc_start: 0.7888 (m-40) cc_final: 0.7475 (m110) REVERT: A 3048 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 3193 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7790 (mm-30) REVERT: A 3195 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8515 (mt-10) REVERT: A 3199 MET cc_start: 0.8511 (ttt) cc_final: 0.8057 (tmm) REVERT: A 3489 TRP cc_start: 0.7658 (m-10) cc_final: 0.7329 (m-10) REVERT: A 3575 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: A 3610 THR cc_start: 0.8390 (p) cc_final: 0.8098 (p) REVERT: A 3747 LYS cc_start: 0.8825 (tmtt) cc_final: 0.8482 (tppt) REVERT: A 3805 SER cc_start: 0.8789 (m) cc_final: 0.8547 (t) REVERT: A 4081 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8693 (t0) REVERT: A 4092 ARG cc_start: 0.8369 (ptm-80) cc_final: 0.8161 (ptm160) REVERT: A 4387 TRP cc_start: 0.7072 (t60) cc_final: 0.6758 (t60) REVERT: A 4469 VAL cc_start: 0.7975 (t) cc_final: 0.7650 (m) outliers start: 37 outliers final: 23 residues processed: 223 average time/residue: 0.1514 time to fit residues: 55.5438 Evaluate side-chains 218 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1733 ILE Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2412 MET Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3575 GLU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4214 SER Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4453 ASN Chi-restraints excluded: chain A residue 4488 GLN Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 248 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1979 GLN ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2913 ASN A2960 GLN A3104 GLN A3584 ASN A3838 ASN A4119 HIS ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4532 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.102874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079994 restraints weight = 59106.048| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.51 r_work: 0.3200 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 22507 Z= 0.255 Angle : 0.667 9.112 30561 Z= 0.331 Chirality : 0.043 0.192 3499 Planarity : 0.005 0.050 3905 Dihedral : 6.250 120.891 3068 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.07 % Allowed : 13.45 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.16), residues: 2755 helix: 1.75 (0.13), residues: 1603 sheet: 0.08 (0.34), residues: 231 loop : -0.69 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A3782 TYR 0.015 0.002 TYR A3812 PHE 0.026 0.002 PHE A3823 TRP 0.017 0.002 TRP A1701 HIS 0.006 0.001 HIS A3155 Details of bonding type rmsd covalent geometry : bond 0.00595 (22507) covalent geometry : angle 0.66663 (30561) hydrogen bonds : bond 0.04017 ( 1299) hydrogen bonds : angle 4.29547 ( 3825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.0072 (mpp) cc_final: -0.0347 (tpt) REVERT: A 1656 LYS cc_start: 0.8466 (ttpt) cc_final: 0.7835 (tttp) REVERT: A 1966 ARG cc_start: 0.8064 (ptm-80) cc_final: 0.7569 (ptp90) REVERT: A 2262 ASP cc_start: 0.8867 (t0) cc_final: 0.8629 (t0) REVERT: A 2479 PHE cc_start: 0.8335 (m-80) cc_final: 0.8048 (m-10) REVERT: A 2500 TRP cc_start: 0.8618 (m100) cc_final: 0.8334 (m100) REVERT: A 2560 HIS cc_start: 0.8827 (t-90) cc_final: 0.8554 (t-90) REVERT: A 2816 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8457 (tp) REVERT: A 2867 MET cc_start: 0.8131 (mmm) cc_final: 0.7899 (mmm) REVERT: A 2936 ILE cc_start: 0.8259 (mm) cc_final: 0.8031 (mm) REVERT: A 3014 ASN cc_start: 0.8032 (m-40) cc_final: 0.7662 (m-40) REVERT: A 3193 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7938 (mm-30) REVERT: A 3195 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8519 (mt-10) REVERT: A 3199 MET cc_start: 0.8576 (ttt) cc_final: 0.8160 (tmm) REVERT: A 3489 TRP cc_start: 0.7754 (m-10) cc_final: 0.7412 (m-10) REVERT: A 3558 GLU cc_start: 0.8205 (pt0) cc_final: 0.7843 (pp20) REVERT: A 3575 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: A 4387 TRP cc_start: 0.7201 (t60) cc_final: 0.6619 (t60) outliers start: 49 outliers final: 32 residues processed: 221 average time/residue: 0.1482 time to fit residues: 53.8753 Evaluate side-chains 204 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2960 GLN Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3575 GLU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4214 SER Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4337 VAL Chi-restraints excluded: chain A residue 4453 ASN Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4488 GLN Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 108 optimal weight: 0.9990 chunk 251 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2085 HIS ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2463 HIS ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3542 GLN ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4477 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 = 0.3762 r_free = 0.3762 target = 0.104530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081756 restraints weight = 58122.925| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.55 r_work: 0.3238 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22507 Z= 0.151 Angle : 0.575 8.715 30561 Z= 0.284 Chirality : 0.040 0.168 3499 Planarity : 0.004 0.043 3905 Dihedral : 6.023 118.789 3068 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.11 % Allowed : 14.51 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.16), residues: 2755 helix: 1.96 (0.13), residues: 1602 sheet: 0.11 (0.35), residues: 230 loop : -0.65 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3782 TYR 0.015 0.001 TYR A2193 PHE 0.020 0.001 PHE A3823 TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00352 (22507) covalent geometry : angle 0.57472 (30561) hydrogen bonds : bond 0.03625 ( 1299) hydrogen bonds : angle 4.08392 ( 3825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.0077 (mpp) cc_final: -0.0301 (tpt) REVERT: A 1656 LYS cc_start: 0.8534 (ttpt) cc_final: 0.7914 (tttp) REVERT: A 1814 GLU cc_start: 0.8518 (tp30) cc_final: 0.8256 (tp30) REVERT: A 1966 ARG cc_start: 0.7970 (ptm-80) cc_final: 0.7486 (ptp90) REVERT: A 2262 ASP cc_start: 0.8904 (t0) cc_final: 0.8473 (t0) REVERT: A 2361 MET cc_start: 0.8862 (mmt) cc_final: 0.8316 (mmp) REVERT: A 2479 PHE cc_start: 0.8297 (m-80) cc_final: 0.8015 (m-10) REVERT: A 2500 TRP cc_start: 0.8606 (m100) cc_final: 0.8316 (m100) REVERT: A 2560 HIS cc_start: 0.8801 (t-90) cc_final: 0.8531 (t-90) REVERT: A 2813 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8985 (tt) REVERT: A 2816 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 3014 ASN cc_start: 0.8078 (m-40) cc_final: 0.7711 (m-40) REVERT: A 3193 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7932 (mm-30) REVERT: A 3195 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8536 (mt-10) REVERT: A 3199 MET cc_start: 0.8595 (ttt) cc_final: 0.8159 (tmm) REVERT: A 3558 GLU cc_start: 0.8072 (pt0) cc_final: 0.7681 (pp20) REVERT: A 3575 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: A 4081 ASP cc_start: 0.9219 (OUTLIER) cc_final: 0.8766 (t0) REVERT: A 4092 ARG cc_start: 0.8346 (ptm-80) cc_final: 0.8122 (ptm160) REVERT: A 4397 HIS cc_start: 0.7383 (m90) cc_final: 0.7091 (m90) REVERT: A 4449 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7885 (ttm-80) outliers start: 50 outliers final: 34 residues processed: 219 average time/residue: 0.1496 time to fit residues: 54.1017 Evaluate side-chains 215 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3479 LEU Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3575 GLU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4214 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4453 ASN Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4488 GLN Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 127 optimal weight: 0.0370 chunk 179 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1950 GLN ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2960 GLN ** A4137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.108340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086078 restraints weight = 58475.281| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.46 r_work: 0.3326 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22507 Z= 0.144 Angle : 0.567 8.879 30561 Z= 0.278 Chirality : 0.040 0.246 3499 Planarity : 0.004 0.045 3905 Dihedral : 5.870 116.653 3068 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.36 % Allowed : 15.06 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.16), residues: 2755 helix: 2.04 (0.13), residues: 1604 sheet: 0.19 (0.35), residues: 229 loop : -0.64 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3782 TYR 0.013 0.001 TYR A4252 PHE 0.021 0.001 PHE A3823 TRP 0.017 0.001 TRP A1701 HIS 0.004 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00335 (22507) covalent geometry : angle 0.56682 (30561) hydrogen bonds : bond 0.03506 ( 1299) hydrogen bonds : angle 4.00653 ( 3825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.0167 (mpp) cc_final: -0.0324 (tpt) REVERT: A 1656 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8046 (tttt) REVERT: A 1814 GLU cc_start: 0.8299 (tp30) cc_final: 0.8077 (tp30) REVERT: A 2262 ASP cc_start: 0.8923 (t0) cc_final: 0.8629 (t0) REVERT: A 2361 MET cc_start: 0.8807 (mmt) cc_final: 0.8296 (mmp) REVERT: A 2373 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8251 (ttm) REVERT: A 2479 PHE cc_start: 0.8296 (m-80) cc_final: 0.8043 (m-10) REVERT: A 2500 TRP cc_start: 0.8567 (m100) cc_final: 0.8311 (m100) REVERT: A 2560 HIS cc_start: 0.8786 (t-90) cc_final: 0.8568 (t-90) REVERT: A 2813 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8951 (tt) REVERT: A 2816 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 2867 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7423 (mtm) REVERT: A 3014 ASN cc_start: 0.8073 (m-40) cc_final: 0.7714 (m-40) REVERT: A 3193 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8069 (mm-30) REVERT: A 3195 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8564 (mt-10) REVERT: A 3199 MET cc_start: 0.8579 (ttt) cc_final: 0.8209 (tmm) REVERT: A 3479 LEU cc_start: 0.8083 (tt) cc_final: 0.7714 (mm) REVERT: A 3575 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: A 4081 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8736 (t0) outliers start: 56 outliers final: 34 residues processed: 230 average time/residue: 0.1510 time to fit residues: 57.0260 Evaluate side-chains 218 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2373 MET Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3575 GLU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4029 HIS Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4214 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4453 ASN Chi-restraints excluded: chain A residue 4488 GLN Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 164 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2960 GLN A4137 ASN ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.109676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.087440 restraints weight = 57929.308| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.44 r_work: 0.3353 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22507 Z= 0.115 Angle : 0.556 9.104 30561 Z= 0.271 Chirality : 0.039 0.189 3499 Planarity : 0.004 0.045 3905 Dihedral : 5.687 112.664 3068 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.90 % Allowed : 16.28 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.16), residues: 2755 helix: 2.14 (0.13), residues: 1603 sheet: 0.28 (0.35), residues: 228 loop : -0.54 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3078 TYR 0.016 0.001 TYR A4252 PHE 0.022 0.001 PHE A3823 TRP 0.017 0.001 TRP A2234 HIS 0.005 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00264 (22507) covalent geometry : angle 0.55594 (30561) hydrogen bonds : bond 0.03327 ( 1299) hydrogen bonds : angle 3.90463 ( 3825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.0200 (mpp) cc_final: -0.0334 (tpt) REVERT: A 1656 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8174 (tttt) REVERT: A 1755 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8188 (mm-40) REVERT: A 2093 LEU cc_start: 0.8770 (tt) cc_final: 0.8545 (tt) REVERT: A 2262 ASP cc_start: 0.8928 (t0) cc_final: 0.8626 (t0) REVERT: A 2361 MET cc_start: 0.8683 (mmt) cc_final: 0.8150 (mmp) REVERT: A 2373 MET cc_start: 0.8447 (ttm) cc_final: 0.8190 (ttm) REVERT: A 2479 PHE cc_start: 0.8265 (m-80) cc_final: 0.8030 (m-10) REVERT: A 2500 TRP cc_start: 0.8564 (m100) cc_final: 0.8252 (m100) REVERT: A 2560 HIS cc_start: 0.8778 (t-90) cc_final: 0.8564 (t-90) REVERT: A 2813 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8928 (tt) REVERT: A 2816 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8568 (tp) REVERT: A 2867 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7256 (mtm) REVERT: A 3014 ASN cc_start: 0.8074 (m-40) cc_final: 0.7769 (m-40) REVERT: A 3193 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8060 (mm-30) REVERT: A 3195 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8613 (mt-10) REVERT: A 3199 MET cc_start: 0.8622 (ttt) cc_final: 0.8218 (tmm) REVERT: A 3479 LEU cc_start: 0.7999 (tt) cc_final: 0.7665 (mm) REVERT: A 3558 GLU cc_start: 0.7885 (pt0) cc_final: 0.7129 (pp20) REVERT: A 3575 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: A 3816 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8142 (tp30) REVERT: A 4081 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8763 (t0) REVERT: A 4397 HIS cc_start: 0.7540 (m90) cc_final: 0.7209 (m90) outliers start: 45 outliers final: 30 residues processed: 219 average time/residue: 0.1481 time to fit residues: 53.9461 Evaluate side-chains 215 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 2018 MET Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3575 GLU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4029 HIS Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4214 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4453 ASN Chi-restraints excluded: chain A residue 4488 GLN Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 193 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2960 GLN ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.110125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.087909 restraints weight = 57902.637| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.44 r_work: 0.3362 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22507 Z= 0.114 Angle : 0.556 9.400 30561 Z= 0.270 Chirality : 0.040 0.289 3499 Planarity : 0.004 0.047 3905 Dihedral : 5.552 109.992 3068 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.69 % Allowed : 16.58 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.16), residues: 2755 helix: 2.18 (0.13), residues: 1608 sheet: 0.35 (0.35), residues: 228 loop : -0.52 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4449 TYR 0.014 0.001 TYR A2641 PHE 0.023 0.001 PHE A3823 TRP 0.016 0.001 TRP A1701 HIS 0.003 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00260 (22507) covalent geometry : angle 0.55621 (30561) hydrogen bonds : bond 0.03275 ( 1299) hydrogen bonds : angle 3.85809 ( 3825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.0152 (mpp) cc_final: -0.0370 (tpt) REVERT: A 2093 LEU cc_start: 0.8780 (tt) cc_final: 0.8564 (tt) REVERT: A 2262 ASP cc_start: 0.8926 (t0) cc_final: 0.8627 (t0) REVERT: A 2373 MET cc_start: 0.8385 (ttm) cc_final: 0.8132 (ttm) REVERT: A 2479 PHE cc_start: 0.8264 (m-80) cc_final: 0.8026 (m-10) REVERT: A 2500 TRP cc_start: 0.8517 (m100) cc_final: 0.8189 (m100) REVERT: A 2560 HIS cc_start: 0.8762 (t-90) cc_final: 0.8548 (t-90) REVERT: A 2813 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8950 (tt) REVERT: A 2816 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8595 (tp) REVERT: A 3014 ASN cc_start: 0.8066 (m-40) cc_final: 0.7753 (m-40) REVERT: A 3193 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8065 (mm-30) REVERT: A 3195 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8629 (mt-10) REVERT: A 3199 MET cc_start: 0.8615 (ttt) cc_final: 0.8223 (tmm) REVERT: A 3479 LEU cc_start: 0.8038 (tt) cc_final: 0.7701 (mm) REVERT: A 3558 GLU cc_start: 0.7895 (pt0) cc_final: 0.7151 (pp20) REVERT: A 3575 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: A 3816 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8195 (tp30) REVERT: A 4081 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8716 (t0) REVERT: A 4397 HIS cc_start: 0.7506 (m90) cc_final: 0.7174 (m90) outliers start: 40 outliers final: 33 residues processed: 211 average time/residue: 0.1531 time to fit residues: 53.1759 Evaluate side-chains 214 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3575 GLU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4029 HIS Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4214 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4453 ASN Chi-restraints excluded: chain A residue 4488 GLN Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 160 optimal weight: 8.9990 chunk 111 optimal weight: 0.0010 chunk 134 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 188 optimal weight: 0.2980 chunk 187 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2445 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 = 0.3876 r_free = 0.3876 target = 0.111391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089292 restraints weight = 57923.206| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.44 r_work: 0.3388 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22507 Z= 0.104 Angle : 0.556 9.298 30561 Z= 0.269 Chirality : 0.039 0.208 3499 Planarity : 0.003 0.046 3905 Dihedral : 5.372 104.976 3068 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.35 % Allowed : 17.04 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.16), residues: 2755 helix: 2.27 (0.13), residues: 1603 sheet: 0.42 (0.35), residues: 228 loop : -0.47 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4449 TYR 0.012 0.001 TYR A2641 PHE 0.025 0.001 PHE A3823 TRP 0.016 0.001 TRP A2234 HIS 0.003 0.000 HIS A1695 Details of bonding type rmsd covalent geometry : bond 0.00231 (22507) covalent geometry : angle 0.55629 (30561) hydrogen bonds : bond 0.03137 ( 1299) hydrogen bonds : angle 3.78363 ( 3825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.0311 (mpp) cc_final: -0.0242 (tpt) REVERT: A 2093 LEU cc_start: 0.8745 (tt) cc_final: 0.8529 (tt) REVERT: A 2262 ASP cc_start: 0.8936 (t0) cc_final: 0.8671 (t0) REVERT: A 2361 MET cc_start: 0.8560 (mmp) cc_final: 0.8233 (mmp) REVERT: A 2479 PHE cc_start: 0.8192 (m-80) cc_final: 0.7939 (m-10) REVERT: A 2560 HIS cc_start: 0.8760 (t-90) cc_final: 0.8542 (t-90) REVERT: A 2813 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8863 (tt) REVERT: A 3014 ASN cc_start: 0.8026 (m-40) cc_final: 0.7715 (m-40) REVERT: A 3193 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8058 (mm-30) REVERT: A 3195 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8621 (mt-10) REVERT: A 3199 MET cc_start: 0.8614 (ttt) cc_final: 0.8220 (tmm) REVERT: A 3479 LEU cc_start: 0.8045 (tt) cc_final: 0.7703 (mm) REVERT: A 3558 GLU cc_start: 0.7838 (pt0) cc_final: 0.7088 (pp20) REVERT: A 3575 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: A 3816 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8153 (tp30) REVERT: A 4081 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8717 (t0) REVERT: A 4397 HIS cc_start: 0.7563 (m90) cc_final: 0.7233 (m90) outliers start: 32 outliers final: 25 residues processed: 218 average time/residue: 0.1534 time to fit residues: 55.5423 Evaluate side-chains 210 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3575 GLU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4029 HIS Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4214 SER Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 164 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 167 optimal weight: 10.0000 chunk 263 optimal weight: 0.0170 chunk 256 optimal weight: 8.9990 chunk 233 optimal weight: 0.0670 chunk 10 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1695 HIS ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2960 GLN ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.108119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085973 restraints weight = 58520.901| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.41 r_work: 0.3327 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22507 Z= 0.174 Angle : 0.604 10.593 30561 Z= 0.295 Chirality : 0.041 0.280 3499 Planarity : 0.004 0.048 3905 Dihedral : 5.514 110.641 3068 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.35 % Allowed : 17.04 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.16), residues: 2755 helix: 2.17 (0.13), residues: 1603 sheet: 0.47 (0.34), residues: 239 loop : -0.54 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4449 TYR 0.015 0.001 TYR A3812 PHE 0.023 0.001 PHE A3823 TRP 0.015 0.001 TRP A1701 HIS 0.005 0.001 HIS A4114 Details of bonding type rmsd covalent geometry : bond 0.00410 (22507) covalent geometry : angle 0.60395 (30561) hydrogen bonds : bond 0.03493 ( 1299) hydrogen bonds : angle 3.93287 ( 3825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 1589 MET cc_start: 0.0155 (mpp) cc_final: -0.0363 (tpt) REVERT: A 1656 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8224 (ttpt) REVERT: A 2262 ASP cc_start: 0.8975 (t0) cc_final: 0.8675 (t0) REVERT: A 2361 MET cc_start: 0.8816 (mmp) cc_final: 0.8437 (mmp) REVERT: A 2479 PHE cc_start: 0.8248 (m-80) cc_final: 0.8007 (m-10) REVERT: A 2560 HIS cc_start: 0.8796 (t-90) cc_final: 0.8566 (t-90) REVERT: A 2816 LEU cc_start: 0.8641 (tp) cc_final: 0.8430 (tp) REVERT: A 3014 ASN cc_start: 0.8159 (m-40) cc_final: 0.7841 (m-40) REVERT: A 3195 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8582 (mt-10) REVERT: A 3199 MET cc_start: 0.8601 (ttt) cc_final: 0.8233 (tmm) REVERT: A 3479 LEU cc_start: 0.8067 (tt) cc_final: 0.7759 (mm) REVERT: A 3558 GLU cc_start: 0.8001 (pt0) cc_final: 0.7658 (pp20) REVERT: A 3575 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: A 3816 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8081 (tp30) REVERT: A 4092 ARG cc_start: 0.8298 (ptm-80) cc_final: 0.7814 (ptm160) REVERT: A 4387 TRP cc_start: 0.8015 (m100) cc_final: 0.7600 (m100) REVERT: A 4397 HIS cc_start: 0.7589 (m90) cc_final: 0.7227 (m90) outliers start: 32 outliers final: 28 residues processed: 203 average time/residue: 0.1492 time to fit residues: 50.3083 Evaluate side-chains 204 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1913 THR Chi-restraints excluded: chain A residue 2095 SER Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2307 VAL Chi-restraints excluded: chain A residue 2568 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3575 GLU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4214 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 58 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 249 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2960 GLN ** A4477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.110095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088040 restraints weight = 58039.828| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.44 r_work: 0.3361 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22507 Z= 0.114 Angle : 0.576 9.466 30561 Z= 0.279 Chirality : 0.039 0.222 3499 Planarity : 0.004 0.045 3905 Dihedral : 5.406 107.122 3068 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.22 % Allowed : 17.33 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.16), residues: 2755 helix: 2.25 (0.13), residues: 1603 sheet: 0.49 (0.34), residues: 238 loop : -0.50 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4591 TYR 0.013 0.001 TYR A3812 PHE 0.024 0.001 PHE A3823 TRP 0.016 0.001 TRP A2234 HIS 0.006 0.001 HIS A1695 Details of bonding type rmsd covalent geometry : bond 0.00258 (22507) covalent geometry : angle 0.57552 (30561) hydrogen bonds : bond 0.03267 ( 1299) hydrogen bonds : angle 3.82783 ( 3825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5389.31 seconds wall clock time: 93 minutes 24.39 seconds (5604.39 seconds total)