Starting phenix.real_space_refine on Fri Sep 19 05:44:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bn5_44722/09_2025/9bn5_44722.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bn5_44722/09_2025/9bn5_44722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bn5_44722/09_2025/9bn5_44722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bn5_44722/09_2025/9bn5_44722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bn5_44722/09_2025/9bn5_44722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bn5_44722/09_2025/9bn5_44722.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 115 5.16 5 C 14728 2.51 5 N 3998 2.21 5 O 4302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23152 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 23040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2866, 23040 Classifications: {'peptide': 2866} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 129, 'TRANS': 2736} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.72, per 1000 atoms: 0.25 Number of scatterers: 23152 At special positions: 0 Unit cell: (129.159, 168.021, 153.162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 115 16.00 P 9 15.00 O 4302 8.00 N 3998 7.00 C 14728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5454 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 20 sheets defined 60.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 1465 through 1470 removed outlier: 3.924A pdb=" N TRP A1470 " --> pdb=" O ILE A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1510 removed outlier: 3.555A pdb=" N LYS A1496 " --> pdb=" O ASP A1492 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A1497 " --> pdb=" O LEU A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1554 removed outlier: 3.746A pdb=" N ASP A1525 " --> pdb=" O LEU A1521 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS A1526 " --> pdb=" O SER A1522 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.630A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1625 removed outlier: 3.651A pdb=" N SER A1625 " --> pdb=" O ARG A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.997A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1693 through 1695 No H-bonds generated for 'chain 'A' and resid 1693 through 1695' Processing helix chain 'A' and resid 1697 through 1730 removed outlier: 4.107A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.855A 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 1773 Processing helix chain 'A' and resid 1776 through 1795 removed outlier: 3.842A pdb=" N SER A1780 " --> pdb=" O ALA A1776 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1828 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 3.691A pdb=" N MET A1941 " --> pdb=" O ASP A1937 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A1942 " --> pdb=" O PHE A1938 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A1946 " --> pdb=" O GLY A1942 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1983 removed outlier: 3.628A pdb=" N ALA A1970 " --> pdb=" O ARG A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 1987 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2076 removed outlier: 3.557A pdb=" N LEU A2065 " --> pdb=" O THR A2061 " (cutoff:3.500A) Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2113 Processing helix chain 'A' and resid 2132 through 2143 removed outlier: 3.534A pdb=" N GLN A2139 " --> pdb=" O GLU A2135 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A2141 " --> pdb=" O LEU A2137 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.130A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A2158 " --> pdb=" O ILE A2154 " (cutoff:3.500A) Processing helix chain 'A' and resid 2181 through 2186 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 2289 Processing helix chain 'A' and resid 2308 through 2313 Processing helix chain 'A' and resid 2315 through 2320 removed outlier: 3.735A pdb=" N ASP A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.519A pdb=" N SER A2384 " --> pdb=" O ALA A2380 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2430 through 2442 removed outlier: 3.886A pdb=" N THR A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2466 Processing helix chain 'A' and resid 2466 through 2476 removed outlier: 3.737A pdb=" N ALA A2470 " --> pdb=" O CYS A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.501A pdb=" N ARG A2488 " --> pdb=" O GLU A2484 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2520 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 removed outlier: 3.780A pdb=" N VAL A2552 " --> pdb=" O GLN A2549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2549 through 2552' Processing helix chain 'A' and resid 2558 through 2562 Processing helix chain 'A' and resid 2576 through 2587 removed outlier: 3.738A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2610 removed outlier: 3.960A pdb=" N ALA A2608 " --> pdb=" O THR A2604 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A2610 " --> pdb=" O PHE A2606 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.096A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 removed outlier: 3.674A pdb=" N MET A2686 " --> pdb=" O PHE A2682 " (cutoff:3.500A) Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 4.227A pdb=" N THR A2750 " --> pdb=" O GLN A2746 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2757 through 2764 Proline residue: A2760 - end of helix removed outlier: 3.760A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2757 through 2764' Processing helix chain 'A' and resid 2765 through 2783 removed outlier: 3.654A pdb=" N ARG A2783 " --> pdb=" O MET A2779 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2810 removed outlier: 3.861A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2866 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.790A pdb=" N VAL A2899 " --> pdb=" O ALA A2895 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.842A 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 2986 through 2988 No H-bonds generated for 'chain 'A' and resid 2986 through 2988' 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 3013 removed outlier: 4.110A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3021 removed outlier: 3.667A pdb=" N LEU A3020 " --> pdb=" O VAL A3017 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A3021 " --> pdb=" O PRO A3018 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3017 through 3021' Processing helix chain 'A' and resid 3023 through 3040 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.626A pdb=" N LEU A3075 " --> pdb=" O SER A3071 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A3077 " --> pdb=" O GLU A3073 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3087 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3139 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.770A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A3194 " --> pdb=" O LYS A3190 " (cutoff:3.500A) Processing helix chain 'A' and resid 3472 through 3517 removed outlier: 3.608A pdb=" N MET A3500 " --> pdb=" O PHE A3496 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3618 through 3630 removed outlier: 3.529A pdb=" N SER A3625 " --> pdb=" O LYS A3621 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A3626 " --> pdb=" O ASN A3622 " (cutoff:3.500A) Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.799A 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 3651 Processing helix chain 'A' and resid 3689 through 3694 Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3734 removed outlier: 3.756A pdb=" N ASP A3725 " --> pdb=" O ARG A3721 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3757 removed outlier: 3.608A pdb=" N ASN A3754 " --> pdb=" O LEU A3750 " (cutoff:3.500A) Processing helix chain 'A' and resid 3763 through 3786 removed outlier: 4.197A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) Processing helix chain 'A' and resid 3792 through 3801 removed outlier: 3.723A pdb=" N THR A3796 " --> pdb=" O GLN A3792 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3818 removed outlier: 3.600A pdb=" N SER A3805 " --> pdb=" O TYR A3801 " (cutoff:3.500A) Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.557A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.559A 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 3911 Processing helix chain 'A' and resid 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3941 removed outlier: 3.666A pdb=" N LEU A3941 " --> pdb=" O ARG A3937 " (cutoff:3.500A) Processing helix chain 'A' and resid 3942 through 3945 removed outlier: 3.600A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3942 through 3945' Processing helix chain 'A' and resid 3947 through 3953 removed outlier: 3.751A pdb=" N ALA A3953 " --> pdb=" O ALA A3949 " (cutoff:3.500A) Processing helix chain 'A' and resid 3955 through 3962 removed outlier: 4.223A pdb=" N ILE A3959 " --> pdb=" O GLU A3955 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3996 Processing helix chain 'A' and resid 3997 through 3999 No H-bonds generated for 'chain 'A' and resid 3997 through 3999' Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.773A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.758A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A4033 " --> pdb=" O HIS A4029 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A4034 " --> pdb=" O ILE A4030 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.762A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4089 removed outlier: 4.021A pdb=" N ASN A4078 " --> pdb=" O ALA A4074 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4113 Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.708A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4166 through 4171 removed outlier: 3.751A pdb=" N LYS A4171 " --> pdb=" O SER A4167 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4196 removed outlier: 3.953A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR A4196 " --> pdb=" O GLU A4192 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.922A 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 4252 through 4256 removed outlier: 3.809A pdb=" N ARG A4255 " --> pdb=" O TYR A4252 " (cutoff:3.500A) Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.595A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4326 through 4345 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.331A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4457 removed outlier: 3.740A pdb=" N LYS A4457 " --> pdb=" O ASN A4453 " (cutoff:3.500A) Processing helix chain 'A' and resid 4461 through 4465 Processing helix chain 'A' and resid 4474 through 4499 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 4532 removed outlier: 3.505A pdb=" N ASN A4532 " --> pdb=" O VAL A4528 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4639 removed outlier: 3.543A pdb=" N GLY A4639 " --> pdb=" O PHE A4635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1478 Processing sheet with id=AA2, first strand: chain 'A' and resid 1664 through 1665 removed outlier: 10.453A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1929 through 1931 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2000 Processing sheet with id=AA7, first strand: chain 'A' and resid 2221 through 2223 removed outlier: 3.727A pdb=" N VAL A2362 " --> pdb=" O MET A2221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2248 through 2251 removed outlier: 7.110A pdb=" N GLU A2248 " --> pdb=" O ARG A2298 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N TRP A2300 " --> pdb=" O GLU A2248 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ARG A2340 " --> pdb=" O LYS A2297 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AB1, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB2, first strand: chain 'A' and resid 2537 through 2538 Processing sheet with id=AB3, first strand: chain 'A' and resid 2615 through 2621 removed outlier: 3.528A pdb=" N PHE A2662 " --> pdb=" O VAL A2618 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A2620 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A2709 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2639 through 2642 removed outlier: 3.926A pdb=" N VAL A2649 " --> pdb=" O ARG A2642 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2872 through 2873 removed outlier: 4.603A pdb=" N LEU A2872 " --> pdb=" O VAL A2884 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.692A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.578A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A3699 " --> pdb=" O LEU A3588 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3661 through 3662 Processing sheet with id=AB9, first strand: chain 'A' and resid 4069 through 4070 removed outlier: 7.001A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.550A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4570 removed outlier: 4.022A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.10 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6880 1.34 - 1.46: 3745 1.46 - 1.58: 12822 1.58 - 1.70: 14 1.70 - 1.82: 192 Bond restraints: 23653 Sorted by residual: bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" N SER A2795 " pdb=" CA SER A2795 " ideal model delta sigma weight residual 1.455 1.486 -0.031 7.00e-03 2.04e+04 1.92e+01 bond pdb=" C5 ADP A4704 " pdb=" C6 ADP A4704 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 23648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 31586 2.50 - 5.01: 435 5.01 - 7.51: 45 7.51 - 10.01: 13 10.01 - 12.51: 6 Bond angle restraints: 32085 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 131.94 7.93 1.00e+00 1.00e+00 6.29e+01 angle pdb=" C MET A2867 " pdb=" CA MET A2867 " pdb=" CB MET A2867 " ideal model delta sigma weight residual 116.54 107.95 8.59 1.15e+00 7.56e-01 5.57e+01 angle pdb=" CA MET A2867 " pdb=" C MET A2867 " pdb=" N SER A2868 " ideal model delta sigma weight residual 119.52 114.84 4.68 7.90e-01 1.60e+00 3.50e+01 angle pdb=" C ALA A1775 " pdb=" CA ALA A1775 " pdb=" CB ALA A1775 " ideal model delta sigma weight residual 115.79 110.32 5.47 1.19e+00 7.06e-01 2.11e+01 angle pdb=" PA ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sigma weight residual 120.50 133.01 -12.51 3.00e+00 1.11e-01 1.74e+01 ... (remaining 32080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.60: 13736 27.60 - 55.20: 510 55.20 - 82.79: 74 82.79 - 110.39: 12 110.39 - 137.99: 2 Dihedral angle restraints: 14334 sinusoidal: 5940 harmonic: 8394 Sorted by residual: dihedral pdb=" O2A ADP A4703 " pdb=" O3A ADP A4703 " pdb=" PA ADP A4703 " pdb=" PB ADP A4703 " ideal model delta sinusoidal sigma weight residual -60.00 77.99 -137.99 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" C2' ADP A4703 " pdb=" C1' ADP A4703 " pdb=" N9 ADP A4703 " pdb=" C4 ADP A4703 " ideal model delta sinusoidal sigma weight residual 91.55 -140.66 -127.79 1 2.00e+01 2.50e-03 3.87e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 41.05 -101.05 1 2.00e+01 2.50e-03 2.86e+01 ... (remaining 14331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2772 0.046 - 0.091: 620 0.091 - 0.137: 186 0.137 - 0.183: 27 0.183 - 0.229: 7 Chirality restraints: 3612 Sorted by residual: chirality pdb=" CB ILE A2759 " pdb=" CA ILE A2759 " pdb=" CG1 ILE A2759 " pdb=" CG2 ILE A2759 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA VAL A1880 " pdb=" N VAL A1880 " pdb=" C VAL A1880 " pdb=" CB VAL A1880 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' ADP A4704 " pdb=" C2' ADP A4704 " pdb=" C4' ADP A4704 " pdb=" O3' ADP A4704 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3609 not shown) Planarity restraints: 4102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A2869 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A2870 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A2870 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A2870 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2526 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO A2527 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A2527 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A2527 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A4172 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO A4173 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A4173 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A4173 " 0.033 5.00e-02 4.00e+02 ... (remaining 4099 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 15 2.28 - 2.93: 9631 2.93 - 3.59: 35911 3.59 - 4.24: 54433 4.24 - 4.90: 91082 Nonbonded interactions: 191072 Sorted by model distance: nonbonded pdb=" O ALA A2742 " pdb=" OE1 GLN A2746 " model vdw 1.624 3.040 nonbonded pdb=" OG1 THR A4033 " pdb=" OE1 GLU A4034 " model vdw 2.143 3.040 nonbonded pdb=" OH TYR A2265 " pdb=" O TRP A2311 " model vdw 2.149 3.040 nonbonded pdb=" O GLU A2294 " pdb=" ND2 ASN A2338 " model vdw 2.157 3.120 nonbonded pdb=" O LEU A4246 " pdb=" OG SER A4250 " model vdw 2.160 3.040 ... (remaining 191067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.270 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 23653 Z= 0.265 Angle : 0.706 12.514 32085 Z= 0.414 Chirality : 0.044 0.229 3612 Planarity : 0.004 0.063 4102 Dihedral : 14.483 137.991 8880 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 0.27 % Allowed : 0.55 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.16), residues: 2854 helix: 1.62 (0.14), residues: 1543 sheet: -1.45 (0.34), residues: 223 loop : -0.71 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2823 TYR 0.018 0.001 TYR A3836 PHE 0.015 0.001 PHE A1534 TRP 0.029 0.001 TRP A4376 HIS 0.005 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00412 (23653) covalent geometry : angle 0.70590 (32085) hydrogen bonds : bond 0.13954 ( 1245) hydrogen bonds : angle 5.57190 ( 3630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 458 time to evaluate : 0.851 Fit side-chains REVERT: A 1557 ILE cc_start: 0.5623 (mm) cc_final: 0.5388 (tp) REVERT: A 2095 SER cc_start: 0.8274 (t) cc_final: 0.7953 (p) REVERT: A 2216 ILE cc_start: 0.7404 (mm) cc_final: 0.7143 (mt) REVERT: A 2485 GLN cc_start: 0.6032 (tt0) cc_final: 0.5411 (tm-30) REVERT: A 2545 TRP cc_start: 0.6680 (m100) cc_final: 0.6179 (m100) REVERT: A 2592 VAL cc_start: 0.7570 (t) cc_final: 0.7139 (t) REVERT: A 2828 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 2831 ARG cc_start: 0.6977 (mmp80) cc_final: 0.6775 (mmt-90) REVERT: A 2839 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 2961 ILE cc_start: 0.7550 (mm) cc_final: 0.6312 (mm) REVERT: A 3034 LYS cc_start: 0.8855 (pttp) cc_final: 0.8224 (tmtt) REVERT: A 3209 LYS cc_start: 0.8258 (mttm) cc_final: 0.7984 (tptm) REVERT: A 3497 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7999 (mtmm) REVERT: A 3861 LYS cc_start: 0.6128 (mtpp) cc_final: 0.5722 (tptt) REVERT: A 3944 PHE cc_start: 0.7376 (m-80) cc_final: 0.6971 (m-80) REVERT: A 4107 MET cc_start: 0.7574 (tpt) cc_final: 0.7368 (tpt) REVERT: A 4111 LYS cc_start: 0.7756 (mmtt) cc_final: 0.7026 (mttt) REVERT: A 4137 ASN cc_start: 0.8144 (t0) cc_final: 0.7450 (t0) REVERT: A 4232 ASN cc_start: 0.7199 (m-40) cc_final: 0.6999 (m-40) REVERT: A 4443 LYS cc_start: 0.7157 (mppt) cc_final: 0.6631 (mmmt) outliers start: 7 outliers final: 3 residues processed: 462 average time/residue: 0.1935 time to fit residues: 135.1767 Evaluate side-chains 264 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1985 HIS A2577 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3197 GLN A3499 GLN A3646 ASN ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3985 GLN A3988 HIS A4065 GLN ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4307 GLN ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4544 ASN A4571 ASN A4573 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.152202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.123127 restraints weight = 38546.089| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.52 r_work: 0.3593 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23653 Z= 0.138 Angle : 0.606 8.896 32085 Z= 0.300 Chirality : 0.041 0.243 3612 Planarity : 0.005 0.074 4102 Dihedral : 6.164 125.344 3188 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 1.33 % Allowed : 7.30 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.16), residues: 2854 helix: 1.63 (0.13), residues: 1584 sheet: -1.48 (0.35), residues: 218 loop : -0.58 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2113 TYR 0.024 0.001 TYR A4636 PHE 0.026 0.002 PHE A4122 TRP 0.019 0.001 TRP A2234 HIS 0.007 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00313 (23653) covalent geometry : angle 0.60603 (32085) hydrogen bonds : bond 0.03883 ( 1245) hydrogen bonds : angle 4.41531 ( 3630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2012 MET cc_start: 0.8729 (ptm) cc_final: 0.8510 (ppp) REVERT: A 2366 GLU cc_start: 0.7650 (tt0) cc_final: 0.6889 (mp0) REVERT: A 2799 MET cc_start: 0.8379 (mtp) cc_final: 0.8172 (mtp) REVERT: A 2831 ARG cc_start: 0.7219 (mmp80) cc_final: 0.6784 (mmt-90) REVERT: A 2839 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 3008 MET cc_start: 0.7936 (mmt) cc_final: 0.7721 (mmt) REVERT: A 3034 LYS cc_start: 0.8823 (pttp) cc_final: 0.8114 (tmtt) REVERT: A 3069 ASN cc_start: 0.7378 (t0) cc_final: 0.6032 (p0) REVERT: A 3164 ARG cc_start: 0.6793 (ttt180) cc_final: 0.6452 (tpt-90) REVERT: A 3209 LYS cc_start: 0.8156 (mttm) cc_final: 0.7912 (tptm) REVERT: A 3497 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8073 (mtmm) REVERT: A 3737 GLU cc_start: 0.5422 (mp0) cc_final: 0.4686 (mm-30) REVERT: A 3861 LYS cc_start: 0.6414 (mtpp) cc_final: 0.5730 (tptt) REVERT: A 3944 PHE cc_start: 0.7509 (m-80) cc_final: 0.6895 (m-80) REVERT: A 4065 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.6058 (pp30) REVERT: A 4095 MET cc_start: 0.7008 (tmm) cc_final: 0.6412 (tmm) REVERT: A 4107 MET cc_start: 0.7655 (tpt) cc_final: 0.6964 (tpt) REVERT: A 4111 LYS cc_start: 0.7542 (mmtt) cc_final: 0.6972 (mttp) REVERT: A 4137 ASN cc_start: 0.7998 (t0) cc_final: 0.7469 (t0) REVERT: A 4232 ASN cc_start: 0.7310 (m-40) cc_final: 0.6976 (m-40) REVERT: A 4443 LYS cc_start: 0.7312 (mppt) cc_final: 0.6807 (mmmt) outliers start: 34 outliers final: 23 residues processed: 296 average time/residue: 0.1729 time to fit residues: 80.9687 Evaluate side-chains 258 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3197 GLN Chi-restraints excluded: chain A residue 3499 GLN Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3710 SER Chi-restraints excluded: chain A residue 4010 SER Chi-restraints excluded: chain A residue 4065 GLN Chi-restraints excluded: chain A residue 4112 LYS Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4612 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 26 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 137 optimal weight: 0.3980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2954 ASN ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4307 GLN ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.150446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121204 restraints weight = 38553.658| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.51 r_work: 0.3562 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23653 Z= 0.147 Angle : 0.574 8.060 32085 Z= 0.285 Chirality : 0.041 0.245 3612 Planarity : 0.004 0.074 4102 Dihedral : 6.063 122.112 3188 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 1.57 % Allowed : 9.38 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 2854 helix: 1.59 (0.13), residues: 1594 sheet: -1.43 (0.35), residues: 204 loop : -0.59 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1843 TYR 0.029 0.002 TYR A3552 PHE 0.019 0.002 PHE A3813 TRP 0.019 0.001 TRP A2234 HIS 0.008 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00344 (23653) covalent geometry : angle 0.57379 (32085) hydrogen bonds : bond 0.03704 ( 1245) hydrogen bonds : angle 4.27370 ( 3630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1602 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.5882 (pt0) REVERT: A 2018 MET cc_start: 0.8518 (mmm) cc_final: 0.8231 (mmm) REVERT: A 2366 GLU cc_start: 0.7777 (tt0) cc_final: 0.7066 (mp0) REVERT: A 2545 TRP cc_start: 0.6513 (m100) cc_final: 0.6189 (m100) REVERT: A 2670 ASP cc_start: 0.5202 (p0) cc_final: 0.4992 (p0) REVERT: A 2831 ARG cc_start: 0.7259 (mmp80) cc_final: 0.6809 (mmt-90) REVERT: A 2839 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 2967 TYR cc_start: 0.7369 (t80) cc_final: 0.6636 (t80) REVERT: A 3030 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7323 (mtp) REVERT: A 3034 LYS cc_start: 0.8827 (pttp) cc_final: 0.8151 (tmtt) REVERT: A 3069 ASN cc_start: 0.7552 (t0) cc_final: 0.6177 (p0) REVERT: A 3164 ARG cc_start: 0.6714 (ttt180) cc_final: 0.6397 (tpt-90) REVERT: A 3209 LYS cc_start: 0.8167 (mttm) cc_final: 0.7893 (tptm) REVERT: A 3802 LEU cc_start: 0.7901 (tp) cc_final: 0.7688 (tp) REVERT: A 3861 LYS cc_start: 0.6588 (mtpp) cc_final: 0.6108 (tptt) REVERT: A 4107 MET cc_start: 0.7674 (tpt) cc_final: 0.7380 (tpt) REVERT: A 4111 LYS cc_start: 0.7563 (mmtt) cc_final: 0.7005 (mttp) REVERT: A 4127 THR cc_start: 0.8592 (m) cc_final: 0.7755 (p) REVERT: A 4137 ASN cc_start: 0.8026 (t0) cc_final: 0.7485 (t0) REVERT: A 4232 ASN cc_start: 0.7312 (m-40) cc_final: 0.6993 (m-40) REVERT: A 4443 LYS cc_start: 0.7219 (mppt) cc_final: 0.6764 (mmmt) REVERT: A 4484 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7693 (mm-30) outliers start: 40 outliers final: 27 residues processed: 274 average time/residue: 0.1623 time to fit residues: 71.1793 Evaluate side-chains 260 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3030 MET Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3710 SER Chi-restraints excluded: chain A residue 4010 SER Chi-restraints excluded: chain A residue 4112 LYS Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4494 LEU Chi-restraints excluded: chain A residue 4612 ASN Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 269 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3499 GLN ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4065 GLN ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.147934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118577 restraints weight = 38382.769| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.49 r_work: 0.3526 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23653 Z= 0.175 Angle : 0.594 10.151 32085 Z= 0.295 Chirality : 0.041 0.223 3612 Planarity : 0.004 0.074 4102 Dihedral : 6.198 122.665 3188 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer: Outliers : 2.16 % Allowed : 11.03 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.16), residues: 2854 helix: 1.50 (0.13), residues: 1592 sheet: -1.55 (0.33), residues: 215 loop : -0.57 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4301 TYR 0.029 0.002 TYR A3552 PHE 0.024 0.002 PHE A3813 TRP 0.021 0.002 TRP A4201 HIS 0.011 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00413 (23653) covalent geometry : angle 0.59401 (32085) hydrogen bonds : bond 0.03752 ( 1245) hydrogen bonds : angle 4.26162 ( 3630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1941 MET cc_start: 0.7118 (mmt) cc_final: 0.6795 (mmt) REVERT: A 2018 MET cc_start: 0.8799 (mmm) cc_final: 0.8487 (mmm) REVERT: A 2670 ASP cc_start: 0.5272 (p0) cc_final: 0.5071 (p0) REVERT: A 2799 MET cc_start: 0.8464 (mtp) cc_final: 0.8245 (mtp) REVERT: A 2839 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7955 (mm-30) REVERT: A 2844 ARG cc_start: 0.8023 (ptt-90) cc_final: 0.7723 (ptp90) REVERT: A 2902 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7267 (mp0) REVERT: A 2967 TYR cc_start: 0.7569 (t80) cc_final: 0.6941 (t80) REVERT: A 3034 LYS cc_start: 0.8818 (pttp) cc_final: 0.8111 (tmtt) REVERT: A 3047 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.6130 (m90) REVERT: A 3209 LYS cc_start: 0.8200 (mttm) cc_final: 0.7884 (tptm) REVERT: A 3861 LYS cc_start: 0.6665 (mtpp) cc_final: 0.6237 (tptt) REVERT: A 4065 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6387 (pp30) REVERT: A 4095 MET cc_start: 0.7316 (tmm) cc_final: 0.6862 (tmm) REVERT: A 4107 MET cc_start: 0.7594 (tpt) cc_final: 0.7344 (tpt) REVERT: A 4127 THR cc_start: 0.8692 (m) cc_final: 0.8288 (t) REVERT: A 4129 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7400 (mt-10) REVERT: A 4137 ASN cc_start: 0.8095 (t0) cc_final: 0.7468 (t0) REVERT: A 4232 ASN cc_start: 0.7320 (m-40) cc_final: 0.7049 (m-40) REVERT: A 4443 LYS cc_start: 0.7206 (mppt) cc_final: 0.6753 (mmmt) REVERT: A 4449 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7799 (mtm-85) outliers start: 55 outliers final: 42 residues processed: 283 average time/residue: 0.1517 time to fit residues: 68.0961 Evaluate side-chains 269 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3694 SER Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3710 SER Chi-restraints excluded: chain A residue 4010 SER Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4065 GLN Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4112 LYS Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4169 ILE Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4337 VAL Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4494 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4612 ASN Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 70 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3527 ASN ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4065 GLN A4100 HIS ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118566 restraints weight = 38462.999| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.51 r_work: 0.3525 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23653 Z= 0.161 Angle : 0.581 8.033 32085 Z= 0.289 Chirality : 0.041 0.263 3612 Planarity : 0.004 0.074 4102 Dihedral : 6.150 122.691 3186 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 2.20 % Allowed : 12.60 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.16), residues: 2854 helix: 1.49 (0.13), residues: 1596 sheet: -1.59 (0.34), residues: 213 loop : -0.59 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4301 TYR 0.025 0.002 TYR A3552 PHE 0.030 0.002 PHE A3629 TRP 0.023 0.001 TRP A4376 HIS 0.008 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00378 (23653) covalent geometry : angle 0.58145 (32085) hydrogen bonds : bond 0.03681 ( 1245) hydrogen bonds : angle 4.20685 ( 3630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 232 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1941 MET cc_start: 0.7153 (mmt) cc_final: 0.6836 (mmt) REVERT: A 2018 MET cc_start: 0.8892 (mmm) cc_final: 0.8575 (mmm) REVERT: A 2281 THR cc_start: 0.8143 (m) cc_final: 0.7753 (p) REVERT: A 2765 TYR cc_start: 0.6864 (m-80) cc_final: 0.6646 (m-80) REVERT: A 2839 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 2844 ARG cc_start: 0.7982 (ptt-90) cc_final: 0.7680 (ptp90) REVERT: A 2967 TYR cc_start: 0.7772 (t80) cc_final: 0.7184 (t80) REVERT: A 3034 LYS cc_start: 0.8828 (pttp) cc_final: 0.8174 (tmtt) REVERT: A 3169 MET cc_start: 0.6290 (tmm) cc_final: 0.5784 (mmt) REVERT: A 3209 LYS cc_start: 0.8199 (mttm) cc_final: 0.7886 (tptm) REVERT: A 3861 LYS cc_start: 0.6797 (mtpp) cc_final: 0.6394 (tptt) REVERT: A 4066 ILE cc_start: 0.6828 (mm) cc_final: 0.6586 (mm) REVERT: A 4095 MET cc_start: 0.7433 (tmm) cc_final: 0.6935 (tmm) REVERT: A 4127 THR cc_start: 0.8690 (m) cc_final: 0.8284 (t) REVERT: A 4129 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7123 (tt0) REVERT: A 4137 ASN cc_start: 0.8092 (t0) cc_final: 0.7462 (t0) REVERT: A 4232 ASN cc_start: 0.7335 (m-40) cc_final: 0.7080 (m-40) REVERT: A 4443 LYS cc_start: 0.7147 (mppt) cc_final: 0.6705 (mmmt) outliers start: 56 outliers final: 42 residues processed: 274 average time/residue: 0.1527 time to fit residues: 67.1788 Evaluate side-chains 262 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1812 ILE Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3506 ASP Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3710 SER Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4010 SER Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4112 LYS Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4337 VAL Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4494 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4612 ASN Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 213 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 101 optimal weight: 0.0970 chunk 117 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3527 ASN A3534 HIS A3602 ASN ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.148649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.119376 restraints weight = 38245.905| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.50 r_work: 0.3534 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23653 Z= 0.133 Angle : 0.559 9.856 32085 Z= 0.276 Chirality : 0.040 0.206 3612 Planarity : 0.004 0.073 4102 Dihedral : 6.090 122.803 3186 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.32 % Allowed : 13.30 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.79 (0.16), residues: 2854 helix: 1.55 (0.13), residues: 1601 sheet: -1.51 (0.34), residues: 215 loop : -0.58 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A4449 TYR 0.029 0.001 TYR A3552 PHE 0.024 0.002 PHE A3629 TRP 0.025 0.001 TRP A4376 HIS 0.006 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00309 (23653) covalent geometry : angle 0.55864 (32085) hydrogen bonds : bond 0.03542 ( 1245) hydrogen bonds : angle 4.13723 ( 3630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1695 HIS cc_start: 0.7449 (m-70) cc_final: 0.6866 (m170) REVERT: A 1941 MET cc_start: 0.7113 (mmt) cc_final: 0.6788 (mmt) REVERT: A 2281 THR cc_start: 0.8112 (m) cc_final: 0.7720 (p) REVERT: A 2839 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7928 (mm-30) REVERT: A 2844 ARG cc_start: 0.7966 (ptt-90) cc_final: 0.7632 (ptp90) REVERT: A 2967 TYR cc_start: 0.7739 (t80) cc_final: 0.7143 (t80) REVERT: A 3034 LYS cc_start: 0.8820 (pttp) cc_final: 0.8163 (tmtt) REVERT: A 3047 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6997 (t-90) REVERT: A 3152 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: A 3169 MET cc_start: 0.6490 (tmm) cc_final: 0.5924 (mmt) REVERT: A 3209 LYS cc_start: 0.8194 (mttm) cc_final: 0.7883 (tptm) REVERT: A 3497 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8026 (mtmm) REVERT: A 3861 LYS cc_start: 0.6720 (mtpp) cc_final: 0.6415 (tptt) REVERT: A 4095 MET cc_start: 0.7368 (tmm) cc_final: 0.6874 (tmm) REVERT: A 4127 THR cc_start: 0.8700 (m) cc_final: 0.8288 (t) REVERT: A 4129 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7083 (tt0) REVERT: A 4137 ASN cc_start: 0.8034 (t0) cc_final: 0.7396 (t0) REVERT: A 4232 ASN cc_start: 0.7348 (m-40) cc_final: 0.7067 (m-40) REVERT: A 4443 LYS cc_start: 0.7217 (mppt) cc_final: 0.6663 (mmmt) outliers start: 59 outliers final: 49 residues processed: 282 average time/residue: 0.1463 time to fit residues: 67.0317 Evaluate side-chains 272 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2983 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3152 GLN Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3694 SER Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3710 SER Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4010 SER Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4112 LYS Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4172 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4494 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4573 ASN Chi-restraints excluded: chain A residue 4612 ASN Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 282 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 261 optimal weight: 0.0870 chunk 276 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1500 HIS A2637 HIS A3047 HIS A3061 ASN ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3534 HIS ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.149649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.120545 restraints weight = 38264.449| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.50 r_work: 0.3551 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23653 Z= 0.119 Angle : 0.551 7.626 32085 Z= 0.273 Chirality : 0.040 0.182 3612 Planarity : 0.004 0.072 4102 Dihedral : 6.042 122.899 3186 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 2.20 % Allowed : 13.89 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 2854 helix: 1.62 (0.13), residues: 1597 sheet: -1.44 (0.34), residues: 215 loop : -0.57 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4449 TYR 0.029 0.001 TYR A3552 PHE 0.021 0.001 PHE A2949 TRP 0.022 0.001 TRP A4376 HIS 0.007 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00271 (23653) covalent geometry : angle 0.55108 (32085) hydrogen bonds : bond 0.03432 ( 1245) hydrogen bonds : angle 4.07237 ( 3630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1695 HIS cc_start: 0.7417 (m-70) cc_final: 0.6872 (m170) REVERT: A 2281 THR cc_start: 0.8130 (m) cc_final: 0.7761 (p) REVERT: A 2783 ARG cc_start: 0.6761 (ptp-170) cc_final: 0.6417 (ptm160) REVERT: A 2839 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7969 (mm-30) REVERT: A 2844 ARG cc_start: 0.7956 (ptt-90) cc_final: 0.7547 (ptp90) REVERT: A 2967 TYR cc_start: 0.7714 (t80) cc_final: 0.7156 (t80) REVERT: A 3034 LYS cc_start: 0.8842 (pttp) cc_final: 0.8226 (tmtt) REVERT: A 3152 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.6716 (mp10) REVERT: A 3169 MET cc_start: 0.6434 (tmm) cc_final: 0.5929 (mmt) REVERT: A 3209 LYS cc_start: 0.8166 (mttm) cc_final: 0.7865 (tptm) REVERT: A 3497 LYS cc_start: 0.8488 (mtmm) cc_final: 0.7994 (mtmm) REVERT: A 3599 PHE cc_start: 0.8375 (t80) cc_final: 0.8084 (t80) REVERT: A 3861 LYS cc_start: 0.6678 (mtpp) cc_final: 0.6359 (tptt) REVERT: A 4095 MET cc_start: 0.7320 (tmm) cc_final: 0.6731 (tmm) REVERT: A 4127 THR cc_start: 0.8641 (m) cc_final: 0.7793 (p) REVERT: A 4129 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7079 (tt0) REVERT: A 4137 ASN cc_start: 0.7938 (t0) cc_final: 0.7331 (t0) REVERT: A 4232 ASN cc_start: 0.7343 (m-40) cc_final: 0.7071 (m-40) REVERT: A 4443 LYS cc_start: 0.7216 (mppt) cc_final: 0.6653 (mmmt) REVERT: A 4451 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6257 (tt) outliers start: 56 outliers final: 47 residues processed: 282 average time/residue: 0.1586 time to fit residues: 72.4255 Evaluate side-chains 271 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2983 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3152 GLN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3506 ASP Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3710 SER Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4010 SER Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4112 LYS Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4172 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4451 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4494 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4612 ASN Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 121 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 chunk 184 optimal weight: 0.4980 chunk 193 optimal weight: 0.8980 chunk 266 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 163 optimal weight: 0.0670 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3214 GLN A3534 HIS ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121100 restraints weight = 37989.406| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.49 r_work: 0.3556 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23653 Z= 0.115 Angle : 0.553 10.563 32085 Z= 0.274 Chirality : 0.040 0.199 3612 Planarity : 0.004 0.071 4102 Dihedral : 6.016 123.036 3186 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 2.16 % Allowed : 14.09 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.16), residues: 2854 helix: 1.68 (0.13), residues: 1597 sheet: -1.34 (0.34), residues: 217 loop : -0.57 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4263 TYR 0.041 0.001 TYR A4636 PHE 0.021 0.001 PHE A3629 TRP 0.021 0.001 TRP A2234 HIS 0.004 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00260 (23653) covalent geometry : angle 0.55337 (32085) hydrogen bonds : bond 0.03360 ( 1245) hydrogen bonds : angle 4.04264 ( 3630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 233 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 1695 HIS cc_start: 0.7388 (m-70) cc_final: 0.6826 (m170) REVERT: A 1750 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7318 (p) REVERT: A 2281 THR cc_start: 0.8074 (m) cc_final: 0.7693 (p) REVERT: A 2545 TRP cc_start: 0.6567 (m100) cc_final: 0.6293 (m100) REVERT: A 2670 ASP cc_start: 0.5307 (p0) cc_final: 0.5086 (p0) REVERT: A 2783 ARG cc_start: 0.6871 (ptp-170) cc_final: 0.6530 (ptm160) REVERT: A 2839 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7955 (mm-30) REVERT: A 2844 ARG cc_start: 0.7954 (ptt-90) cc_final: 0.7519 (ptp90) REVERT: A 2967 TYR cc_start: 0.7652 (t80) cc_final: 0.7152 (t80) REVERT: A 3034 LYS cc_start: 0.8860 (pttp) cc_final: 0.8275 (tmtt) REVERT: A 3152 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6864 (mp10) REVERT: A 3169 MET cc_start: 0.6349 (tmm) cc_final: 0.5912 (mmt) REVERT: A 3209 LYS cc_start: 0.8173 (mttm) cc_final: 0.7887 (tptm) REVERT: A 3497 LYS cc_start: 0.8479 (mtmm) cc_final: 0.7996 (mtmm) REVERT: A 3861 LYS cc_start: 0.6603 (mtpp) cc_final: 0.6294 (tptt) REVERT: A 4095 MET cc_start: 0.7309 (tmm) cc_final: 0.6761 (tmm) REVERT: A 4127 THR cc_start: 0.8708 (m) cc_final: 0.7889 (p) REVERT: A 4129 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7086 (tt0) REVERT: A 4137 ASN cc_start: 0.7920 (t0) cc_final: 0.7310 (t0) REVERT: A 4232 ASN cc_start: 0.7289 (m-40) cc_final: 0.6988 (m-40) REVERT: A 4443 LYS cc_start: 0.7193 (mppt) cc_final: 0.6633 (mmmt) outliers start: 55 outliers final: 49 residues processed: 277 average time/residue: 0.1615 time to fit residues: 72.7358 Evaluate side-chains 273 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2983 SER Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3152 GLN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3506 ASP Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3710 SER Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4010 SER Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4112 LYS Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4172 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4451 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4612 ASN Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 164 optimal weight: 2.9990 chunk 104 optimal weight: 0.0000 chunk 233 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 109 optimal weight: 0.0170 chunk 184 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 68 optimal weight: 0.0470 chunk 214 optimal weight: 6.9990 overall best weight: 0.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 HIS ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.152508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123614 restraints weight = 38381.484| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.50 r_work: 0.3595 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23653 Z= 0.102 Angle : 0.542 12.263 32085 Z= 0.266 Chirality : 0.039 0.152 3612 Planarity : 0.004 0.071 4102 Dihedral : 5.890 123.062 3186 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 1.92 % Allowed : 14.68 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.16), residues: 2854 helix: 1.84 (0.13), residues: 1600 sheet: -0.99 (0.36), residues: 202 loop : -0.60 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4263 TYR 0.028 0.001 TYR A3552 PHE 0.040 0.001 PHE A3599 TRP 0.033 0.001 TRP A4376 HIS 0.005 0.000 HIS A3200 Details of bonding type rmsd covalent geometry : bond 0.00221 (23653) covalent geometry : angle 0.54206 (32085) hydrogen bonds : bond 0.03143 ( 1245) hydrogen bonds : angle 3.92327 ( 3630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1695 HIS cc_start: 0.7334 (m-70) cc_final: 0.6902 (m170) REVERT: A 2281 THR cc_start: 0.8042 (m) cc_final: 0.7541 (p) REVERT: A 2324 LEU cc_start: 0.8591 (pp) cc_final: 0.8189 (mt) REVERT: A 2366 GLU cc_start: 0.7602 (tt0) cc_final: 0.7020 (mp0) REVERT: A 2545 TRP cc_start: 0.6468 (m100) cc_final: 0.6196 (m100) REVERT: A 2670 ASP cc_start: 0.5379 (p0) cc_final: 0.5093 (p0) REVERT: A 2819 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6070 (mm-30) REVERT: A 2839 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7948 (mm-30) REVERT: A 2967 TYR cc_start: 0.7624 (t80) cc_final: 0.7130 (t80) REVERT: A 3034 LYS cc_start: 0.8852 (pttp) cc_final: 0.8268 (tmtt) REVERT: A 3047 HIS cc_start: 0.6774 (t70) cc_final: 0.6361 (t-90) REVERT: A 3135 GLN cc_start: 0.6520 (pm20) cc_final: 0.6238 (pp30) REVERT: A 3169 MET cc_start: 0.6307 (tmm) cc_final: 0.5993 (mmt) REVERT: A 3209 LYS cc_start: 0.8095 (mttm) cc_final: 0.7823 (tptm) REVERT: A 3500 MET cc_start: 0.6831 (mmp) cc_final: 0.6618 (mmp) REVERT: A 3861 LYS cc_start: 0.6549 (mtpp) cc_final: 0.6150 (tptt) REVERT: A 4095 MET cc_start: 0.7243 (tmm) cc_final: 0.6794 (tmm) REVERT: A 4127 THR cc_start: 0.8658 (m) cc_final: 0.7832 (p) REVERT: A 4129 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7072 (tt0) REVERT: A 4137 ASN cc_start: 0.7800 (t0) cc_final: 0.7196 (t0) REVERT: A 4232 ASN cc_start: 0.7271 (m-40) cc_final: 0.6946 (m-40) REVERT: A 4443 LYS cc_start: 0.7149 (mppt) cc_final: 0.6607 (mmmt) outliers start: 49 outliers final: 37 residues processed: 283 average time/residue: 0.1520 time to fit residues: 69.6562 Evaluate side-chains 262 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2819 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3506 ASP Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4451 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4612 ASN Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 119 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 102 optimal weight: 0.0060 chunk 111 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS ** A3709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3880 HIS A4054 HIS ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.150965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.122013 restraints weight = 38283.259| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.50 r_work: 0.3574 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23653 Z= 0.117 Angle : 0.555 9.662 32085 Z= 0.272 Chirality : 0.039 0.163 3612 Planarity : 0.004 0.069 4102 Dihedral : 5.898 122.393 3186 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 1.53 % Allowed : 14.95 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.16), residues: 2854 helix: 1.82 (0.13), residues: 1593 sheet: -0.97 (0.36), residues: 211 loop : -0.55 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3873 TYR 0.031 0.001 TYR A3552 PHE 0.037 0.001 PHE A3599 TRP 0.028 0.001 TRP A4376 HIS 0.006 0.001 HIS A3200 Details of bonding type rmsd covalent geometry : bond 0.00269 (23653) covalent geometry : angle 0.55502 (32085) hydrogen bonds : bond 0.03225 ( 1245) hydrogen bonds : angle 3.95402 ( 3630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1695 HIS cc_start: 0.7350 (m-70) cc_final: 0.6848 (m170) REVERT: A 2281 THR cc_start: 0.8114 (m) cc_final: 0.7707 (p) REVERT: A 2324 LEU cc_start: 0.8588 (pp) cc_final: 0.8247 (mt) REVERT: A 2366 GLU cc_start: 0.7635 (tt0) cc_final: 0.7051 (mp0) REVERT: A 2670 ASP cc_start: 0.5352 (p0) cc_final: 0.5138 (p0) REVERT: A 2819 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6010 (mm-30) REVERT: A 2839 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 2967 TYR cc_start: 0.7726 (t80) cc_final: 0.7257 (t80) REVERT: A 3034 LYS cc_start: 0.8875 (pttp) cc_final: 0.8283 (tmtt) REVERT: A 3047 HIS cc_start: 0.6800 (t70) cc_final: 0.6425 (t-90) REVERT: A 3135 GLN cc_start: 0.6540 (pm20) cc_final: 0.6280 (pp30) REVERT: A 3169 MET cc_start: 0.6328 (tmm) cc_final: 0.6042 (mmt) REVERT: A 3209 LYS cc_start: 0.7888 (mttm) cc_final: 0.7651 (tptm) REVERT: A 3500 MET cc_start: 0.6866 (mmp) cc_final: 0.6649 (mmp) REVERT: A 3861 LYS cc_start: 0.6556 (mtpp) cc_final: 0.6194 (tptt) REVERT: A 4095 MET cc_start: 0.7306 (tmm) cc_final: 0.6755 (tmm) REVERT: A 4127 THR cc_start: 0.8662 (m) cc_final: 0.7898 (p) REVERT: A 4129 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7081 (tt0) REVERT: A 4137 ASN cc_start: 0.7827 (t0) cc_final: 0.7229 (t0) REVERT: A 4232 ASN cc_start: 0.7251 (m-40) cc_final: 0.6970 (m-40) REVERT: A 4443 LYS cc_start: 0.7151 (mppt) cc_final: 0.6615 (mmmt) REVERT: A 4454 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7027 (mm-30) outliers start: 39 outliers final: 36 residues processed: 255 average time/residue: 0.1561 time to fit residues: 65.1359 Evaluate side-chains 260 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2356 VAL Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2819 GLU Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3202 ASN Chi-restraints excluded: chain A residue 3506 ASP Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3547 ILE Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4451 LEU Chi-restraints excluded: chain A residue 4474 THR Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4573 ASN Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 69 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 200 optimal weight: 0.3980 chunk 273 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS A3499 GLN A3709 GLN A4054 HIS ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.150883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121886 restraints weight = 38267.893| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.50 r_work: 0.3569 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23653 Z= 0.119 Angle : 0.556 8.920 32085 Z= 0.273 Chirality : 0.039 0.159 3612 Planarity : 0.004 0.070 4102 Dihedral : 5.918 122.147 3186 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 1.65 % Allowed : 14.99 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.16), residues: 2854 helix: 1.82 (0.13), residues: 1593 sheet: -0.97 (0.36), residues: 211 loop : -0.54 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3873 TYR 0.029 0.001 TYR A3552 PHE 0.034 0.002 PHE A3599 TRP 0.029 0.001 TRP A4376 HIS 0.006 0.001 HIS A3200 Details of bonding type rmsd covalent geometry : bond 0.00274 (23653) covalent geometry : angle 0.55571 (32085) hydrogen bonds : bond 0.03237 ( 1245) hydrogen bonds : angle 3.96311 ( 3630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5446.45 seconds wall clock time: 94 minutes 15.79 seconds (5655.79 seconds total)