Starting phenix.real_space_refine on Thu May 22 22:52:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bn3_44720/05_2025/9bn3_44720.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bn3_44720/05_2025/9bn3_44720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bn3_44720/05_2025/9bn3_44720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bn3_44720/05_2025/9bn3_44720.map" model { file = "/net/cci-nas-00/data/ceres_data/9bn3_44720/05_2025/9bn3_44720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bn3_44720/05_2025/9bn3_44720.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.050 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 84 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.75, per 1000 atoms: 0.55 Number of scatterers: 23152 At special positions: 0 Unit cell: (130.621, 168.433, 152.391, 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: 6.11 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 124 helices and 20 sheets defined 60.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 1465 through 1470 removed outlier: 3.958A pdb=" N TRP A1470 " --> pdb=" O ILE A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1510 removed outlier: 3.552A pdb=" N LYS A1496 " --> pdb=" O ASP A1492 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL A1497 " --> pdb=" O LEU A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1554 removed outlier: 3.824A pdb=" N ASP A1525 " --> pdb=" O LEU A1521 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A1526 " --> pdb=" O SER A1522 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.626A 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: 3.599A 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: 3.839A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 3.776A 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 1697 through 1730 removed outlier: 4.062A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.901A 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 1797 removed outlier: 3.728A pdb=" N SER A1780 " --> pdb=" O ALA A1776 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (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: 3.529A pdb=" N MET A1941 " --> pdb=" O ASP A1937 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A1942 " --> pdb=" O PHE A1938 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) removed outlier: 3.608A 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 1984 removed outlier: 3.742A pdb=" N ALA A1970 " --> pdb=" O ARG A1966 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A1984 " --> pdb=" O GLU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 1987 No H-bonds generated for 'chain 'A' and resid 1985 through 1987' Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2077 Proline residue: A2071 - end of helix removed outlier: 3.649A pdb=" N ASP A2077 " --> pdb=" O PHE A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2113 Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 3.559A pdb=" N THR A2144 " --> pdb=" O SER A2140 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.073A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2186 removed outlier: 3.706A pdb=" N GLU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A2183 " --> pdb=" O ARG A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2289 Processing helix chain 'A' and resid 2308 through 2313 removed outlier: 3.537A pdb=" N VAL A2312 " --> pdb=" O ASP A2308 " (cutoff:3.500A) Processing helix chain 'A' and resid 2315 through 2320 removed outlier: 3.898A 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 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2430 through 2442 removed outlier: 3.910A pdb=" N THR A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.754A pdb=" N VAL A2469 " --> pdb=" O ALA A2465 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A2470 " --> pdb=" O CYS A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.511A pdb=" N ARG A2488 " --> pdb=" O GLU A2484 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.681A 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 2571 through 2587 removed outlier: 3.569A pdb=" N ARG A2576 " --> pdb=" O LEU A2572 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A2578 " --> pdb=" O THR A2574 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A2579 " --> pdb=" O VAL A2575 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2610 removed outlier: 3.831A pdb=" N ALA A2608 " --> pdb=" O THR A2604 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A2610 " --> pdb=" O PHE A2606 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.077A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 removed outlier: 3.568A 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: 4.006A pdb=" N THR A2750 " --> pdb=" O GLN A2746 " (cutoff:3.500A) removed outlier: 3.938A 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: 3.677A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 5.458A 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: 3.740A pdb=" N ARG A2783 " --> pdb=" O MET A2779 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2809 removed outlier: 3.789A 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 removed outlier: 3.547A pdb=" N ALA A2866 " --> pdb=" O ARG A2863 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.769A pdb=" N VAL A2899 " --> pdb=" O ALA A2895 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.855A 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 3001 through 3014 removed outlier: 4.065A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) 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: 3.830A pdb=" N ASP A3077 " --> pdb=" O GLU A3073 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3086 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3139 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.568A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A3194 " --> pdb=" O LYS A3190 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3472 through 3517 removed outlier: 3.616A pdb=" N MET A3500 " --> pdb=" O PHE A3496 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.250A 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 3553 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 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.611A 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: 3.737A pdb=" N ASP A3725 " --> pdb=" O ARG A3721 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3757 removed outlier: 3.612A pdb=" N ASN A3754 " --> pdb=" O LEU A3750 " (cutoff:3.500A) Processing helix chain 'A' and resid 3763 through 3786 removed outlier: 4.168A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) Processing helix chain 'A' and resid 3793 through 3801 Processing helix chain 'A' and resid 3801 through 3818 Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.515A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A3842 " --> pdb=" O ASN A3838 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.560A 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: 3.699A pdb=" N LEU A3941 " --> pdb=" O ARG A3937 " (cutoff:3.500A) Processing helix chain 'A' and resid 3942 through 3945 removed outlier: 3.712A 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: 3.819A pdb=" N ALA A3953 " --> pdb=" O ALA A3949 " (cutoff:3.500A) Processing helix chain 'A' and resid 3955 through 3962 removed outlier: 4.412A 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: 3.810A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.697A 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 4035 removed outlier: 3.805A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A4033 " --> pdb=" O HIS A4029 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A4035 " --> pdb=" O VAL A4031 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 4.085A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4089 removed outlier: 3.990A pdb=" N ASN A4078 " --> pdb=" O ALA A4074 " (cutoff:3.500A) removed outlier: 4.312A 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 4142 removed outlier: 3.516A 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 4165 through 4171 removed outlier: 3.673A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A4171 " --> pdb=" O SER A4167 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4193 removed outlier: 4.158A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.772A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 removed outlier: 3.602A pdb=" N GLN A4262 " --> pdb=" O ASN A4258 " (cutoff:3.500A) Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.552A 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 4346 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4407 through 4440 Processing helix chain 'A' and resid 4445 through 4457 removed outlier: 3.711A 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 Processing helix chain 'A' and resid 4631 through 4638 removed outlier: 3.522A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (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 1663 through 1666 removed outlier: 6.594A pdb=" N SER A1663 " --> pdb=" O ILE A1676 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A1676 " --> pdb=" O SER A1663 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A1665 " --> pdb=" O LEU A1674 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.115A 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 removed outlier: 6.097A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.378A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2000 Processing sheet with id=AA7, first strand: chain 'A' and resid 2221 through 2223 removed outlier: 3.785A 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: 7.074A pdb=" N GLU A2248 " --> pdb=" O ARG A2298 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N TRP A2300 " --> pdb=" O GLU A2248 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ARG A2340 " --> pdb=" O LYS A2297 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.128A 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 removed outlier: 3.651A pdb=" N THR A2267 " --> pdb=" O THR A2276 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A2276 " --> pdb=" O THR A2267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 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: 3.673A pdb=" N LEU A2620 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2639 through 2642 removed outlier: 4.013A pdb=" N VAL A2649 " --> pdb=" O ARG A2642 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.357A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.378A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3661 through 3662 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.163A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A4128 " --> pdb=" O MET A4043 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 6.658A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N CYS A4286 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS A4292 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.548A 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: 3.912A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1258 hydrogen bonds defined for protein. 3675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.34 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7621 1.35 - 1.46: 5311 1.46 - 1.58: 10517 1.58 - 1.70: 12 1.70 - 1.82: 192 Bond restraints: 23653 Sorted by residual: bond pdb=" CG PRO A3587 " pdb=" CD PRO A3587 " ideal model delta sigma weight residual 1.503 1.300 0.203 3.40e-02 8.65e+02 3.56e+01 bond pdb=" C LEU A2668 " pdb=" N PRO A2669 " ideal model delta sigma weight residual 1.331 1.367 -0.036 1.27e-02 6.20e+03 7.96e+00 bond pdb=" CB PRO A3966 " pdb=" CG PRO A3966 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.37e+00 bond pdb=" N PRO A3587 " pdb=" CD PRO A3587 " ideal model delta sigma weight residual 1.473 1.501 -0.028 1.40e-02 5.10e+03 3.86e+00 bond pdb=" CB ARG A3628 " pdb=" CG ARG A3628 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.79e+00 ... (remaining 23648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 31902 3.29 - 6.59: 166 6.59 - 9.88: 10 9.88 - 13.18: 5 13.18 - 16.47: 2 Bond angle restraints: 32085 Sorted by residual: angle pdb=" N PRO A3587 " pdb=" CD PRO A3587 " pdb=" CG PRO A3587 " ideal model delta sigma weight residual 103.20 86.73 16.47 1.50e+00 4.44e-01 1.21e+02 angle pdb=" CA PRO A3587 " pdb=" CB PRO A3587 " pdb=" CG PRO A3587 " ideal model delta sigma weight residual 104.50 88.05 16.45 1.90e+00 2.77e-01 7.50e+01 angle pdb=" N PRO A3587 " pdb=" CA PRO A3587 " pdb=" CB PRO A3587 " ideal model delta sigma weight residual 103.35 98.07 5.28 8.70e-01 1.32e+00 3.69e+01 angle pdb=" CA PRO A3587 " pdb=" N PRO A3587 " pdb=" CD PRO A3587 " ideal model delta sigma weight residual 112.00 104.34 7.66 1.40e+00 5.10e-01 2.99e+01 angle pdb=" N VAL A3128 " pdb=" CA VAL A3128 " pdb=" C VAL A3128 " ideal model delta sigma weight residual 112.12 108.24 3.88 8.40e-01 1.42e+00 2.14e+01 ... (remaining 32080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.46: 13508 25.46 - 50.93: 733 50.93 - 76.39: 71 76.39 - 101.85: 20 101.85 - 127.32: 2 Dihedral angle restraints: 14334 sinusoidal: 5940 harmonic: 8394 Sorted by residual: 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 -141.13 -127.32 1 2.00e+01 2.50e-03 3.85e+01 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 61.55 -121.55 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" CA GLU A3737 " pdb=" C GLU A3737 " pdb=" N PHE A3738 " pdb=" CA PHE A3738 " ideal model delta harmonic sigma weight residual 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 14331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2418 0.035 - 0.071: 855 0.071 - 0.106: 267 0.106 - 0.142: 68 0.142 - 0.177: 4 Chirality restraints: 3612 Sorted by residual: chirality pdb=" CB VAL A2853 " pdb=" CA VAL A2853 " pdb=" CG1 VAL A2853 " pdb=" CG2 VAL A2853 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CG LEU A4264 " pdb=" CB LEU A4264 " pdb=" CD1 LEU A4264 " pdb=" CD2 LEU A4264 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA ILE A4238 " pdb=" N ILE A4238 " pdb=" C ILE A4238 " pdb=" CB ILE A4238 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 3609 not shown) Planarity restraints: 4102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A1776 " 0.044 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO A1777 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A1777 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1777 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A2869 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO A2870 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A2870 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A2870 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A2759 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO A2760 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A2760 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A2760 " 0.034 5.00e-02 4.00e+02 ... (remaining 4099 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 455 2.70 - 3.25: 23723 3.25 - 3.80: 38159 3.80 - 4.35: 50073 4.35 - 4.90: 81616 Nonbonded interactions: 194026 Sorted by model distance: nonbonded pdb=" OG1 THR A4033 " pdb=" OE1 GLU A4034 " model vdw 2.146 3.040 nonbonded pdb=" O MET A3113 " pdb=" NH2 ARG A3140 " model vdw 2.178 3.120 nonbonded pdb=" OH TYR A2265 " pdb=" O TRP A2311 " model vdw 2.192 3.040 nonbonded pdb=" ND2 ASN A3158 " pdb=" O MET A3169 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASP A3730 " pdb=" NZ LYS A3733 " model vdw 2.212 3.120 ... (remaining 194021 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 59.190 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 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 0.203 23653 Z= 0.152 Angle : 0.673 16.471 32085 Z= 0.353 Chirality : 0.041 0.177 3612 Planarity : 0.005 0.068 4102 Dihedral : 14.892 127.318 8880 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 2854 helix: 1.48 (0.13), residues: 1551 sheet: -0.61 (0.35), residues: 241 loop : -0.64 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A4376 HIS 0.010 0.001 HIS A4029 PHE 0.029 0.002 PHE A1926 TYR 0.015 0.002 TYR A3183 ARG 0.008 0.001 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.13466 ( 1258) hydrogen bonds : angle 5.46505 ( 3675) covalent geometry : bond 0.00353 (23653) covalent geometry : angle 0.67294 (32085) *********************** 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 349 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 2.510 Fit side-chains revert: symmetry clash REVERT: A 2172 ARG cc_start: 0.7137 (ttt-90) cc_final: 0.6859 (tmt170) REVERT: A 2373 MET cc_start: 0.8107 (mtp) cc_final: 0.7742 (mtp) outliers start: 1 outliers final: 2 residues processed: 348 average time/residue: 1.2283 time to fit residues: 497.4741 Evaluate side-chains 253 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 251 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1941 MET Chi-restraints excluded: chain A residue 3077 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 146 optimal weight: 0.0060 chunk 115 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 259 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2005 GLN A2109 GLN A3534 HIS A3540 ASN ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4065 GLN ** A4117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4612 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.202979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.168429 restraints weight = 27715.532| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.67 r_work: 0.3820 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1016 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= 0.131 Angle : 0.598 9.856 32085 Z= 0.297 Chirality : 0.041 0.139 3612 Planarity : 0.005 0.067 4102 Dihedral : 6.455 128.785 3188 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 1.77 % Allowed : 8.52 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2854 helix: 1.61 (0.13), residues: 1574 sheet: -0.57 (0.34), residues: 241 loop : -0.50 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.008 0.001 HIS A3880 PHE 0.019 0.002 PHE A1926 TYR 0.016 0.001 TYR A1745 ARG 0.008 0.000 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 1258) hydrogen bonds : angle 4.36654 ( 3675) covalent geometry : bond 0.00289 (23653) covalent geometry : angle 0.59843 (32085) *********************** 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 367 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 time to evaluate : 2.620 Fit side-chains revert: symmetry clash REVERT: A 1931 ASN cc_start: 0.8060 (t0) cc_final: 0.7835 (t0) REVERT: A 2315 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7064 (mp) REVERT: A 2373 MET cc_start: 0.8128 (mtp) cc_final: 0.7738 (mtp) REVERT: A 2620 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6349 (tt) REVERT: A 2763 ARG cc_start: 0.6441 (mmm-85) cc_final: 0.6173 (mmp-170) REVERT: A 3005 LEU cc_start: 0.6331 (mt) cc_final: 0.5863 (pp) REVERT: A 3078 ARG cc_start: 0.7941 (tpp-160) cc_final: 0.7732 (tpp-160) REVERT: A 3862 ASP cc_start: 0.7502 (t0) cc_final: 0.7127 (t0) REVERT: A 4101 LEU cc_start: 0.7460 (mt) cc_final: 0.7252 (mt) REVERT: A 4257 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: A 4292 LYS cc_start: 0.7772 (mtmm) cc_final: 0.6926 (tmmt) outliers start: 45 outliers final: 19 residues processed: 343 average time/residue: 1.3583 time to fit residues: 537.2079 Evaluate side-chains 282 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2248 GLU Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3537 GLN Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3708 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4257 ASP Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 251 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2698 GLN A2752 ASN A2791 HIS ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3534 HIS A3540 ASN ** A3880 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4065 GLN A4117 GLN A4612 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.199620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.165040 restraints weight = 27545.781| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.67 r_work: 0.3773 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23653 Z= 0.150 Angle : 0.605 10.695 32085 Z= 0.299 Chirality : 0.041 0.187 3612 Planarity : 0.005 0.065 4102 Dihedral : 6.382 127.970 3183 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 2.51 % Allowed : 12.48 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.16), residues: 2854 helix: 1.61 (0.13), residues: 1576 sheet: -0.65 (0.34), residues: 241 loop : -0.46 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.009 0.001 HIS A1810 PHE 0.020 0.002 PHE A3813 TYR 0.024 0.002 TYR A3026 ARG 0.009 0.001 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 1258) hydrogen bonds : angle 4.24876 ( 3675) covalent geometry : bond 0.00348 (23653) covalent geometry : angle 0.60548 (32085) *********************** 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 352 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6238 (mmp) cc_final: 0.5977 (mpm) REVERT: A 1613 LYS cc_start: 0.7362 (tptp) cc_final: 0.6809 (ttpm) REVERT: A 1667 ASN cc_start: 0.6510 (t0) cc_final: 0.6300 (t0) REVERT: A 1849 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7221 (mmpt) REVERT: A 2212 GLN cc_start: 0.7869 (mm110) cc_final: 0.7597 (pt0) REVERT: A 2315 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7138 (mp) REVERT: A 2373 MET cc_start: 0.8159 (mtp) cc_final: 0.7896 (mtp) REVERT: A 2448 ASP cc_start: 0.7528 (m-30) cc_final: 0.7266 (m-30) REVERT: A 2582 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: A 2620 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6334 (tt) REVERT: A 3005 LEU cc_start: 0.6225 (mt) cc_final: 0.5839 (pp) REVERT: A 3199 MET cc_start: 0.6261 (ppp) cc_final: 0.5299 (ppp) REVERT: A 4095 MET cc_start: 0.7448 (ttt) cc_final: 0.7112 (ttt) REVERT: A 4101 LEU cc_start: 0.7543 (mt) cc_final: 0.7254 (mt) REVERT: A 4257 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7184 (m-30) outliers start: 64 outliers final: 21 residues processed: 324 average time/residue: 1.3325 time to fit residues: 498.3346 Evaluate side-chains 277 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1849 LYS Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2852 THR Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 4117 GLN Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4257 ASP Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 276 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2083 GLN ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3534 HIS A3540 ASN A3880 HIS A4065 GLN A4117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.195338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.159886 restraints weight = 27713.453| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.70 r_work: 0.3717 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23653 Z= 0.199 Angle : 0.651 11.060 32085 Z= 0.321 Chirality : 0.043 0.162 3612 Planarity : 0.005 0.068 4102 Dihedral : 6.634 128.868 3183 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.45 % Allowed : 13.74 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2854 helix: 1.38 (0.13), residues: 1583 sheet: -0.68 (0.33), residues: 243 loop : -0.54 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2234 HIS 0.011 0.002 HIS A3880 PHE 0.025 0.002 PHE A3813 TYR 0.018 0.002 TYR A2638 ARG 0.009 0.001 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 1258) hydrogen bonds : angle 4.34098 ( 3675) covalent geometry : bond 0.00479 (23653) covalent geometry : angle 0.65071 (32085) *********************** 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 358 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 270 time to evaluate : 2.881 Fit side-chains REVERT: A 1589 MET cc_start: 0.6167 (mmp) cc_final: 0.5942 (mpm) REVERT: A 1613 LYS cc_start: 0.7274 (tptp) cc_final: 0.6757 (ttpm) REVERT: A 1667 ASN cc_start: 0.6512 (t0) cc_final: 0.6084 (t0) REVERT: A 1814 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7819 (tp30) REVERT: A 2212 GLN cc_start: 0.7984 (mm110) cc_final: 0.7699 (pt0) REVERT: A 2315 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7001 (mp) REVERT: A 2444 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: A 2448 ASP cc_start: 0.7596 (m-30) cc_final: 0.7327 (m-30) REVERT: A 2582 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6431 (m-80) REVERT: A 2620 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6335 (tt) REVERT: A 3005 LEU cc_start: 0.6340 (mt) cc_final: 0.5963 (pp) REVERT: A 3052 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6674 (tmmt) REVERT: A 3199 MET cc_start: 0.6418 (ppp) cc_final: 0.5600 (ppp) REVERT: A 3627 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6532 (mt) REVERT: A 3699 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8278 (m) REVERT: A 3799 GLN cc_start: 0.6876 (mm-40) cc_final: 0.6617 (tm-30) REVERT: A 3815 MET cc_start: 0.8156 (mtp) cc_final: 0.7682 (mtp) REVERT: A 3915 VAL cc_start: 0.5708 (OUTLIER) cc_final: 0.5316 (t) REVERT: A 4095 MET cc_start: 0.7720 (ttt) cc_final: 0.7508 (ttt) REVERT: A 4209 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: A 4287 LYS cc_start: 0.8005 (mtmt) cc_final: 0.6748 (mttp) REVERT: A 4307 GLN cc_start: 0.8292 (mt0) cc_final: 0.8084 (mt0) REVERT: A 4514 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7963 (mt) outliers start: 88 outliers final: 38 residues processed: 325 average time/residue: 1.3290 time to fit residues: 498.1985 Evaluate side-chains 287 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2248 GLU Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2415 ILE Chi-restraints excluded: chain A residue 2434 THR Chi-restraints excluded: chain A residue 2444 GLU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2583 THR Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2852 THR Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3052 LYS Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3537 GLN Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3648 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 224 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1784 ASN A2031 ASN A2725 HIS A2954 ASN A3522 GLN A3534 HIS A3636 GLN A3700 ASN A3772 ASN A4065 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.196974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.161396 restraints weight = 27624.301| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.65 r_work: 0.3736 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23653 Z= 0.137 Angle : 0.596 10.681 32085 Z= 0.293 Chirality : 0.040 0.186 3612 Planarity : 0.004 0.066 4102 Dihedral : 6.457 127.322 3183 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 2.63 % Allowed : 15.97 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2854 helix: 1.58 (0.13), residues: 1573 sheet: -0.65 (0.33), residues: 242 loop : -0.46 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2234 HIS 0.007 0.001 HIS A2637 PHE 0.017 0.002 PHE A3813 TYR 0.019 0.001 TYR A2638 ARG 0.009 0.000 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 1258) hydrogen bonds : angle 4.20898 ( 3675) covalent geometry : bond 0.00320 (23653) covalent geometry : angle 0.59633 (32085) *********************** 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 334 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 267 time to evaluate : 2.628 Fit side-chains revert: symmetry clash REVERT: A 1613 LYS cc_start: 0.7242 (tptp) cc_final: 0.6742 (ttpm) REVERT: A 1667 ASN cc_start: 0.6458 (t0) cc_final: 0.6095 (t0) REVERT: A 1964 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6998 (pt0) REVERT: A 2212 GLN cc_start: 0.7994 (mm110) cc_final: 0.7692 (pt0) REVERT: A 2315 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7009 (mp) REVERT: A 2373 MET cc_start: 0.8219 (mtp) cc_final: 0.7707 (mtp) REVERT: A 2448 ASP cc_start: 0.7780 (m-30) cc_final: 0.7558 (m-30) REVERT: A 2582 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: A 2620 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6374 (tt) REVERT: A 3005 LEU cc_start: 0.6314 (mt) cc_final: 0.5974 (pp) REVERT: A 3052 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6726 (tmmt) REVERT: A 3199 MET cc_start: 0.6354 (ppp) cc_final: 0.6066 (pp-130) REVERT: A 3627 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6607 (mt) REVERT: A 3699 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8240 (m) REVERT: A 3799 GLN cc_start: 0.6772 (mm-40) cc_final: 0.6502 (tm-30) REVERT: A 3815 MET cc_start: 0.8124 (mtp) cc_final: 0.7672 (mtp) REVERT: A 4095 MET cc_start: 0.7672 (ttt) cc_final: 0.7304 (ttt) REVERT: A 4157 MET cc_start: 0.8797 (mtp) cc_final: 0.8507 (mtt) REVERT: A 4209 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7037 (pm20) REVERT: A 4287 LYS cc_start: 0.7984 (mtmt) cc_final: 0.6711 (mttp) REVERT: A 4307 GLN cc_start: 0.8295 (mt0) cc_final: 0.8081 (mt0) outliers start: 67 outliers final: 37 residues processed: 313 average time/residue: 1.3545 time to fit residues: 490.5402 Evaluate side-chains 288 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2248 GLU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2654 GLN Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3052 LYS Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3537 GLN Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4209 GLU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 139 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1832 ASN A2031 ASN A2849 ASN A3534 HIS A3622 ASN A4065 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.159950 restraints weight = 27541.964| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.67 r_work: 0.3728 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23653 Z= 0.169 Angle : 0.627 10.934 32085 Z= 0.307 Chirality : 0.041 0.172 3612 Planarity : 0.005 0.068 4102 Dihedral : 6.496 127.995 3183 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 3.10 % Allowed : 16.41 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.16), residues: 2854 helix: 1.54 (0.13), residues: 1566 sheet: -0.69 (0.33), residues: 244 loop : -0.53 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2234 HIS 0.007 0.001 HIS A2637 PHE 0.026 0.002 PHE A3599 TYR 0.017 0.001 TYR A2748 ARG 0.009 0.000 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1258) hydrogen bonds : angle 4.23755 ( 3675) covalent geometry : bond 0.00402 (23653) covalent geometry : angle 0.62723 (32085) *********************** 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 338 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 259 time to evaluate : 2.481 Fit side-chains revert: symmetry clash REVERT: A 1613 LYS cc_start: 0.7218 (tptp) cc_final: 0.6748 (ttpm) REVERT: A 1931 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8189 (t0) REVERT: A 1964 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: A 2172 ARG cc_start: 0.7555 (tmt90) cc_final: 0.7334 (tmt-80) REVERT: A 2212 GLN cc_start: 0.8001 (mm110) cc_final: 0.7666 (pt0) REVERT: A 2315 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7058 (mp) REVERT: A 2373 MET cc_start: 0.8193 (mtp) cc_final: 0.7749 (mtp) REVERT: A 2582 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: A 2620 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6371 (tt) REVERT: A 3005 LEU cc_start: 0.6265 (mt) cc_final: 0.5919 (pp) REVERT: A 3052 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6742 (tmmt) REVERT: A 3199 MET cc_start: 0.6455 (ppp) cc_final: 0.5745 (ppp) REVERT: A 3627 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6746 (mt) REVERT: A 3698 PHE cc_start: 0.8142 (m-80) cc_final: 0.7865 (m-10) REVERT: A 3699 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8261 (m) REVERT: A 3799 GLN cc_start: 0.6669 (mm-40) cc_final: 0.6409 (tm-30) REVERT: A 3915 VAL cc_start: 0.5653 (OUTLIER) cc_final: 0.5266 (t) REVERT: A 4095 MET cc_start: 0.7788 (ttt) cc_final: 0.7488 (ttt) REVERT: A 4157 MET cc_start: 0.8855 (mtp) cc_final: 0.8580 (mtt) REVERT: A 4287 LYS cc_start: 0.8031 (mtmt) cc_final: 0.6864 (mttp) REVERT: A 4307 GLN cc_start: 0.8276 (mt0) cc_final: 0.8064 (mt0) REVERT: A 4514 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7940 (mt) outliers start: 79 outliers final: 43 residues processed: 310 average time/residue: 1.3195 time to fit residues: 473.4993 Evaluate side-chains 293 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1931 ASN Chi-restraints excluded: chain A residue 1964 GLU Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2091 ARG Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2248 GLU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2654 GLN Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2852 THR Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3052 LYS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3537 GLN Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3648 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3784 VAL Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 194 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 232 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3152 GLN A3534 HIS A4065 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.195801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.160214 restraints weight = 27520.065| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.69 r_work: 0.3735 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23653 Z= 0.148 Angle : 0.610 10.715 32085 Z= 0.298 Chirality : 0.041 0.195 3612 Planarity : 0.005 0.067 4102 Dihedral : 6.353 127.343 3183 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 2.98 % Allowed : 17.31 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 2854 helix: 1.62 (0.13), residues: 1565 sheet: -0.68 (0.33), residues: 244 loop : -0.52 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2234 HIS 0.010 0.001 HIS A2637 PHE 0.029 0.002 PHE A3599 TYR 0.016 0.001 TYR A2748 ARG 0.010 0.000 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1258) hydrogen bonds : angle 4.17535 ( 3675) covalent geometry : bond 0.00349 (23653) covalent geometry : angle 0.60996 (32085) *********************** 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 335 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 259 time to evaluate : 2.634 Fit side-chains REVERT: A 1613 LYS cc_start: 0.7028 (tptp) cc_final: 0.6609 (ttpm) REVERT: A 1931 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8148 (t0) REVERT: A 2212 GLN cc_start: 0.7985 (mm110) cc_final: 0.7640 (pt0) REVERT: A 2315 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7034 (mp) REVERT: A 2373 MET cc_start: 0.8177 (mtp) cc_final: 0.7752 (mtp) REVERT: A 2582 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6378 (m-80) REVERT: A 2620 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6368 (tt) REVERT: A 3005 LEU cc_start: 0.6332 (mt) cc_final: 0.5968 (pp) REVERT: A 3052 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6753 (tmmt) REVERT: A 3152 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7024 (mt0) REVERT: A 3156 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: A 3199 MET cc_start: 0.6524 (ppp) cc_final: 0.6007 (ppp) REVERT: A 3627 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6829 (mt) REVERT: A 3699 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8253 (m) REVERT: A 3799 GLN cc_start: 0.6660 (mm-40) cc_final: 0.6390 (tm-30) REVERT: A 3915 VAL cc_start: 0.5599 (OUTLIER) cc_final: 0.5209 (t) REVERT: A 4095 MET cc_start: 0.7802 (ttt) cc_final: 0.7460 (ttt) REVERT: A 4124 LEU cc_start: 0.8406 (tt) cc_final: 0.8167 (tp) REVERT: A 4157 MET cc_start: 0.8864 (mtp) cc_final: 0.8545 (mtt) REVERT: A 4307 GLN cc_start: 0.8251 (mt0) cc_final: 0.8038 (mt0) REVERT: A 4514 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8017 (mt) outliers start: 76 outliers final: 42 residues processed: 311 average time/residue: 1.3266 time to fit residues: 477.6093 Evaluate side-chains 293 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1931 ASN Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2091 ARG Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2654 GLN Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2852 THR Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3052 LYS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3152 GLN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3537 GLN Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3699 VAL Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3784 VAL Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 276 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 274 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 151 optimal weight: 0.0060 chunk 280 optimal weight: 0.0060 chunk 7 optimal weight: 6.9990 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3522 GLN A3534 HIS ** A3622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4065 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.198032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.163035 restraints weight = 27422.905| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.66 r_work: 0.3749 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23653 Z= 0.118 Angle : 0.588 10.182 32085 Z= 0.287 Chirality : 0.040 0.206 3612 Planarity : 0.004 0.070 4102 Dihedral : 6.159 126.504 3183 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.08 % Favored : 96.85 % Rotamer: Outliers : 2.47 % Allowed : 18.05 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 2854 helix: 1.75 (0.13), residues: 1568 sheet: -0.59 (0.33), residues: 245 loop : -0.41 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2234 HIS 0.009 0.001 HIS A2637 PHE 0.017 0.001 PHE A3599 TYR 0.014 0.001 TYR A1546 ARG 0.010 0.000 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 1258) hydrogen bonds : angle 4.08250 ( 3675) covalent geometry : bond 0.00268 (23653) covalent geometry : angle 0.58789 (32085) *********************** 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 326 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 263 time to evaluate : 2.484 Fit side-chains revert: symmetry clash REVERT: A 1613 LYS cc_start: 0.6941 (tptp) cc_final: 0.6598 (ttpm) REVERT: A 1931 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8157 (t0) REVERT: A 2168 VAL cc_start: 0.7344 (OUTLIER) cc_final: 0.7073 (t) REVERT: A 2172 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6648 (tmt-80) REVERT: A 2212 GLN cc_start: 0.8020 (mm110) cc_final: 0.7497 (pt0) REVERT: A 2315 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7104 (mp) REVERT: A 2373 MET cc_start: 0.8161 (mtp) cc_final: 0.7710 (mtp) REVERT: A 2582 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6396 (m-80) REVERT: A 2620 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6434 (tt) REVERT: A 3005 LEU cc_start: 0.6372 (mt) cc_final: 0.6033 (pp) REVERT: A 3052 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6768 (tmmt) REVERT: A 3199 MET cc_start: 0.6420 (ppp) cc_final: 0.5917 (ppp) REVERT: A 3627 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7035 (mt) REVERT: A 3799 GLN cc_start: 0.6499 (mm-40) cc_final: 0.6201 (tm-30) REVERT: A 3915 VAL cc_start: 0.5538 (OUTLIER) cc_final: 0.5160 (t) REVERT: A 4095 MET cc_start: 0.7771 (ttt) cc_final: 0.7391 (ttt) REVERT: A 4124 LEU cc_start: 0.8421 (tt) cc_final: 0.8175 (tp) REVERT: A 4157 MET cc_start: 0.8832 (mtp) cc_final: 0.8491 (mtt) REVERT: A 4158 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 4307 GLN cc_start: 0.8248 (mt0) cc_final: 0.8037 (mt0) REVERT: A 4514 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7897 (mt) outliers start: 63 outliers final: 33 residues processed: 306 average time/residue: 1.3077 time to fit residues: 464.0272 Evaluate side-chains 290 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1931 ASN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2091 ARG Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2852 THR Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3052 LYS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 76 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2637 HIS A2781 GLN A3152 GLN A3534 HIS A3622 ASN A3845 ASN A4131 ASN A4612 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.193236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.157417 restraints weight = 27501.676| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.67 r_work: 0.3700 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 23653 Z= 0.201 Angle : 0.675 10.702 32085 Z= 0.333 Chirality : 0.044 0.244 3612 Planarity : 0.005 0.066 4102 Dihedral : 6.462 125.465 3183 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.51 % Allowed : 18.45 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2854 helix: 1.41 (0.13), residues: 1575 sheet: -0.73 (0.33), residues: 237 loop : -0.57 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2234 HIS 0.012 0.001 HIS A2637 PHE 0.028 0.002 PHE A3599 TYR 0.021 0.002 TYR A2748 ARG 0.011 0.001 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1258) hydrogen bonds : angle 4.33060 ( 3675) covalent geometry : bond 0.00479 (23653) covalent geometry : angle 0.67512 (32085) *********************** 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 319 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 2.884 Fit side-chains revert: symmetry clash REVERT: A 1613 LYS cc_start: 0.6977 (tptp) cc_final: 0.6604 (ttpm) REVERT: A 1931 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8225 (t0) REVERT: A 2172 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6613 (tmt-80) REVERT: A 2212 GLN cc_start: 0.8018 (mm110) cc_final: 0.7435 (pt0) REVERT: A 2315 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7036 (mp) REVERT: A 2373 MET cc_start: 0.8151 (mtp) cc_final: 0.7748 (mtp) REVERT: A 2582 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: A 2620 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6393 (tt) REVERT: A 3005 LEU cc_start: 0.6447 (mt) cc_final: 0.6014 (pp) REVERT: A 3052 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6807 (tmmt) REVERT: A 3199 MET cc_start: 0.6605 (ppp) cc_final: 0.6093 (ppp) REVERT: A 3536 LEU cc_start: 0.8055 (mp) cc_final: 0.7750 (mt) REVERT: A 3627 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7299 (mt) REVERT: A 3799 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6430 (tm-30) REVERT: A 3915 VAL cc_start: 0.5498 (OUTLIER) cc_final: 0.5111 (t) REVERT: A 4117 GLN cc_start: 0.5249 (OUTLIER) cc_final: 0.4914 (pm20) REVERT: A 4503 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6362 (tp30) REVERT: A 4514 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8052 (mt) outliers start: 64 outliers final: 39 residues processed: 297 average time/residue: 1.3537 time to fit residues: 464.2814 Evaluate side-chains 285 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1931 ASN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2091 ARG Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2852 THR Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3052 LYS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3537 GLN Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3648 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4117 GLN Chi-restraints excluded: chain A residue 4146 VAL Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 91 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 219 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 226 optimal weight: 0.1980 chunk 175 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1832 ASN A2377 ASN A2637 HIS A3534 HIS A3845 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.195817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.160288 restraints weight = 27523.735| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.65 r_work: 0.3741 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 23653 Z= 0.135 Angle : 0.630 10.469 32085 Z= 0.309 Chirality : 0.041 0.254 3612 Planarity : 0.005 0.066 4102 Dihedral : 6.287 122.629 3183 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 2.08 % Allowed : 19.00 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2854 helix: 1.57 (0.13), residues: 1578 sheet: -0.70 (0.33), residues: 238 loop : -0.48 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2234 HIS 0.011 0.001 HIS A2637 PHE 0.016 0.002 PHE A3599 TYR 0.022 0.001 TYR A3516 ARG 0.008 0.000 ARG A4140 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1258) hydrogen bonds : angle 4.22136 ( 3675) covalent geometry : bond 0.00316 (23653) covalent geometry : angle 0.62965 (32085) ********************** 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 300 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 2.885 Fit side-chains REVERT: A 1613 LYS cc_start: 0.6869 (tptp) cc_final: 0.6587 (ttpm) REVERT: A 1709 MET cc_start: 0.8228 (ttp) cc_final: 0.8021 (tmm) REVERT: A 1931 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8136 (t0) REVERT: A 2172 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6698 (tmt-80) REVERT: A 2212 GLN cc_start: 0.7966 (mm110) cc_final: 0.7624 (pt0) REVERT: A 2315 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6945 (mp) REVERT: A 2373 MET cc_start: 0.8111 (mtp) cc_final: 0.7700 (mtp) REVERT: A 2582 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6381 (m-80) REVERT: A 2620 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6256 (tt) REVERT: A 3005 LEU cc_start: 0.6427 (mt) cc_final: 0.6018 (pp) REVERT: A 3052 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6789 (tmmt) REVERT: A 3156 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7142 (mp-120) REVERT: A 3199 MET cc_start: 0.6554 (ppp) cc_final: 0.6073 (ppp) REVERT: A 3536 LEU cc_start: 0.8009 (mp) cc_final: 0.7727 (mt) REVERT: A 3627 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7275 (mt) REVERT: A 3799 GLN cc_start: 0.6518 (mm-40) cc_final: 0.6305 (tm-30) REVERT: A 3915 VAL cc_start: 0.5517 (OUTLIER) cc_final: 0.5143 (t) REVERT: A 4307 GLN cc_start: 0.8256 (mt0) cc_final: 0.8020 (mt0) REVERT: A 4503 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6313 (tp30) outliers start: 53 outliers final: 38 residues processed: 282 average time/residue: 1.2508 time to fit residues: 410.8555 Evaluate side-chains 290 residues out of total 2551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1931 ASN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2091 ARG Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2315 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2582 TYR Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2620 LEU Chi-restraints excluded: chain A residue 2653 VAL Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2852 THR Chi-restraints excluded: chain A residue 2902 GLU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3050 LEU Chi-restraints excluded: chain A residue 3052 LYS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3627 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4089 LYS Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4296 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 25 optimal weight: 3.9990 chunk 242 optimal weight: 0.0010 chunk 8 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1832 ASN A2377 ASN ** A2637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3534 HIS A3845 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.195981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160828 restraints weight = 27390.015| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.65 r_work: 0.3737 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 23653 Z= 0.154 Angle : 0.750 59.197 32085 Z= 0.402 Chirality : 0.042 0.370 3612 Planarity : 0.005 0.066 4102 Dihedral : 6.292 122.611 3183 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 2.08 % Allowed : 19.00 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2854 helix: 1.57 (0.13), residues: 1578 sheet: -0.70 (0.33), residues: 238 loop : -0.51 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2234 HIS 0.009 0.001 HIS A2637 PHE 0.018 0.002 PHE A3599 TYR 0.031 0.001 TYR A3516 ARG 0.010 0.000 ARG A3728 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 1258) hydrogen bonds : angle 4.22163 ( 3675) covalent geometry : bond 0.00359 (23653) covalent geometry : angle 0.74988 (32085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17906.58 seconds wall clock time: 308 minutes 39.68 seconds (18519.68 seconds total)