Starting phenix.real_space_refine on Fri Jun 20 08:29:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm6_44689/06_2025/9bm6_44689.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm6_44689/06_2025/9bm6_44689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bm6_44689/06_2025/9bm6_44689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm6_44689/06_2025/9bm6_44689.map" model { file = "/net/cci-nas-00/data/ceres_data/9bm6_44689/06_2025/9bm6_44689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm6_44689/06_2025/9bm6_44689.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 1 5.21 5 S 115 5.16 5 C 14703 2.51 5 N 3987 2.21 5 O 4295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23111 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2858, 22994 Classifications: {'peptide': 2858} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 129, 'TRANS': 2728} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {' MG': 1, 'ADP': 2, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 13.83, per 1000 atoms: 0.60 Number of scatterers: 23111 At special positions: 0 Unit cell: (150.592, 148.928, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 10 15.00 Mg 1 11.99 O 4295 8.00 N 3987 7.00 C 14703 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: 5.96 Conformation dependent library (CDL) restraints added in 3.0 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 20 sheets defined 61.9% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 1460 through 1472 Processing helix chain 'A' and resid 1489 through 1510 Processing helix chain 'A' and resid 1512 through 1552 removed outlier: 4.236A pdb=" N PHE A1516 " --> pdb=" O TYR A1512 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU A1518 " --> pdb=" O LYS A1514 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP A1519 " --> pdb=" O VAL A1515 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A1544 " --> pdb=" O VAL A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 Processing helix chain 'A' and resid 1561 through 1584 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1631 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1650 removed outlier: 3.652A pdb=" N LYS A1649 " --> pdb=" O ASN A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.815A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A1658 " --> pdb=" O PHE A1654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1653 through 1658' Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.718A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1777 through 1797 removed outlier: 3.641A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1824 removed outlier: 3.535A pdb=" N SER A1824 " --> pdb=" O ASP A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 4.498A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1985 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2079 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2113 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.227A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 removed outlier: 3.742A pdb=" N GLU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2230 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2315 through 2320 removed outlier: 3.542A 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 2365 through 2369 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.616A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2502 removed outlier: 3.652A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 Processing helix chain 'A' and resid 2571 through 2586 Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.631A pdb=" N THR A2604 " --> pdb=" O GLY A2600 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.105A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2757 removed outlier: 3.543A pdb=" N ARG A2757 " --> pdb=" O ARG A2753 " (cutoff:3.500A) Processing helix chain 'A' and resid 2758 through 2764 removed outlier: 6.629A pdb=" N SER A2761 " --> pdb=" O LEU A2758 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2783 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.743A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.501A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.529A pdb=" N LEU A2889 " --> pdb=" O ASP A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 Processing helix chain 'A' and resid 2942 through 2955 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.828A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3083 through 3087 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 4.126A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3472 through 3502 Processing helix chain 'A' and resid 3503 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.998A pdb=" N TYR A3552 " --> pdb=" O ALA A3548 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) No H-bonds generated for '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 3627 Processing helix chain 'A' and resid 3637 through 3641 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3694 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3735 removed outlier: 4.016A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3757 Processing helix chain 'A' and resid 3762 through 3786 removed outlier: 3.759A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3818 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.595A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.837A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 4.221A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3875 through 3878 removed outlier: 5.970A pdb=" N GLN A3878 " --> pdb=" O MET A3875 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3875 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3928 through 3940 Processing helix chain 'A' and resid 3941 through 3945 removed outlier: 3.577A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.548A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (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 4013 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.530A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) Processing helix chain 'A' and resid 4027 through 4033 Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.929A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4091 removed outlier: 4.028A pdb=" N ASN A4078 " --> pdb=" O ALA A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4114 Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.636A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4196 removed outlier: 3.876A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR A4196 " --> pdb=" O GLU A4192 " (cutoff:3.500A) Processing helix chain 'A' and resid 4197 through 4202 removed outlier: 3.510A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.609A 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 4249 Processing helix chain 'A' and resid 4250 through 4255 removed outlier: 3.997A pdb=" N ARG A4255 " --> pdb=" O TYR A4252 " (cutoff:3.500A) Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.581A 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 4325 through 4346 removed outlier: 4.412A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 removed outlier: 3.640A pdb=" N LYS A4457 " --> pdb=" O ASN A4453 " (cutoff:3.500A) Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4516 through 4531 Processing helix chain 'A' and resid 4532 through 4534 No H-bonds generated for 'chain 'A' and resid 4532 through 4534' Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 removed outlier: 3.525A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.777A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 6.741A pdb=" N SER A1677 " --> pdb=" O SER A1662 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE A1664 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLY A1675 " --> pdb=" O ILE A1664 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A1666 " --> pdb=" O VAL A1673 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A1673 " --> pdb=" O LEU A1666 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A1690 " --> pdb=" O VAL A1673 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1903 removed outlier: 6.267A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (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 1930 removed outlier: 6.108A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2253 removed outlier: 6.282A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2621 removed outlier: 5.995A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2642 removed outlier: 3.602A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.646A pdb=" N SER A2874 " --> pdb=" O ILE A2882 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.601A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.159A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3661 through 3664 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 5.792A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 6.585A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N CYS A4286 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 7.307A 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: 9.992A pdb=" N VAL A4509 " --> pdb=" O SER A4557 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A4559 " --> pdb=" O VAL A4509 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.811A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1325 hydrogen bonds defined for protein. 3852 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: 14.58 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7595 1.34 - 1.46: 5278 1.46 - 1.58: 10533 1.58 - 1.70: 13 1.70 - 1.82: 192 Bond restraints: 23611 Sorted by residual: bond pdb=" N LEU A2387 " pdb=" CA LEU A2387 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.35e+00 bond pdb=" C SER A4172 " pdb=" N PRO A4173 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.27e-02 6.20e+03 5.15e+00 bond pdb=" CB CYS A2454 " pdb=" SG CYS A2454 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.83e+00 bond pdb=" N ASP A2388 " pdb=" CA ASP A2388 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.63e+00 bond pdb=" CA GLY A3165 " pdb=" C GLY A3165 " ideal model delta sigma weight residual 1.530 1.516 0.015 1.04e-02 9.25e+03 2.00e+00 ... (remaining 23606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 31913 3.35 - 6.70: 104 6.70 - 10.05: 11 10.05 - 13.40: 0 13.40 - 16.75: 1 Bond angle restraints: 32029 Sorted by residual: angle pdb=" C ASP A3045 " pdb=" CA ASP A3045 " pdb=" CB ASP A3045 " ideal model delta sigma weight residual 116.63 109.98 6.65 1.16e+00 7.43e-01 3.29e+01 angle pdb=" CA LEU A4451 " pdb=" CB LEU A4451 " pdb=" CG LEU A4451 " ideal model delta sigma weight residual 116.30 133.05 -16.75 3.50e+00 8.16e-02 2.29e+01 angle pdb=" CA MET A1507 " pdb=" CB MET A1507 " pdb=" CG MET A1507 " ideal model delta sigma weight residual 114.10 120.81 -6.71 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CA ASP A3045 " pdb=" C ASP A3045 " pdb=" N SER A3046 " ideal model delta sigma weight residual 119.63 116.96 2.67 8.10e-01 1.52e+00 1.09e+01 angle pdb=" CB MET A3043 " pdb=" CG MET A3043 " pdb=" SD MET A3043 " ideal model delta sigma weight residual 112.70 122.43 -9.73 3.00e+00 1.11e-01 1.05e+01 ... (remaining 32024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 12311 18.03 - 36.06: 1498 36.06 - 54.09: 399 54.09 - 72.12: 88 72.12 - 90.15: 29 Dihedral angle restraints: 14325 sinusoidal: 5954 harmonic: 8371 Sorted by residual: dihedral pdb=" CA LEU A1533 " pdb=" C LEU A1533 " pdb=" N PHE A1534 " pdb=" CA PHE A1534 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 13.54 -73.54 1 2.00e+01 2.50e-03 1.72e+01 dihedral pdb=" CA LYS A2865 " pdb=" C LYS A2865 " pdb=" N ALA A2866 " pdb=" CA ALA A2866 " ideal model delta harmonic sigma weight residual 180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 14322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2764 0.042 - 0.083: 608 0.083 - 0.125: 218 0.125 - 0.166: 12 0.166 - 0.208: 1 Chirality restraints: 3603 Sorted by residual: chirality pdb=" CB THR A3502 " pdb=" CA THR A3502 " pdb=" OG1 THR A3502 " pdb=" CG2 THR A3502 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE A2138 " pdb=" CA ILE A2138 " pdb=" CG1 ILE A2138 " pdb=" CG2 ILE A2138 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE A2882 " pdb=" N ILE A2882 " pdb=" C ILE A2882 " pdb=" CB ILE A2882 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 3600 not shown) Planarity restraints: 4094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1531 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C MET A1531 " -0.034 2.00e-02 2.50e+03 pdb=" O MET A1531 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A1532 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A2773 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C MET A2773 " -0.033 2.00e-02 2.50e+03 pdb=" O MET A2773 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A2774 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A4172 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO A4173 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A4173 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A4173 " 0.027 5.00e-02 4.00e+02 ... (remaining 4091 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 209 2.60 - 3.17: 19915 3.17 - 3.75: 37640 3.75 - 4.32: 50038 4.32 - 4.90: 84246 Nonbonded interactions: 192048 Sorted by model distance: nonbonded pdb=" OG1 THR A2602 " pdb="MG MG A4705 " model vdw 2.020 2.170 nonbonded pdb=" O2G ATP A4703 " pdb="MG MG A4705 " model vdw 2.032 2.170 nonbonded pdb=" O TYR A4447 " pdb=" OG1 THR A4450 " model vdw 2.157 3.040 nonbonded pdb=" O ALA A2497 " pdb=" OG SER A2501 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A2231 " pdb=" O1B ATP A4702 " model vdw 2.198 3.040 ... (remaining 192043 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: 5.010 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: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 59.200 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23611 Z= 0.127 Angle : 0.570 16.751 32029 Z= 0.294 Chirality : 0.039 0.208 3603 Planarity : 0.004 0.048 4094 Dihedral : 17.272 90.147 8885 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 0.35 % Allowed : 21.50 % Favored : 78.14 % 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: 1.37 (0.16), residues: 2844 helix: 1.79 (0.13), residues: 1585 sheet: -0.61 (0.35), residues: 233 loop : -0.03 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A4376 HIS 0.004 0.000 HIS A1817 PHE 0.014 0.001 PHE A3813 TYR 0.024 0.001 TYR A2170 ARG 0.008 0.000 ARG A3682 Details of bonding type rmsd hydrogen bonds : bond 0.12805 ( 1325) hydrogen bonds : angle 5.49293 ( 3852) covalent geometry : bond 0.00261 (23611) covalent geometry : angle 0.56993 (32029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 235 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1967 MET cc_start: 0.8257 (mmp) cc_final: 0.7880 (tpt) outliers start: 9 outliers final: 4 residues processed: 240 average time/residue: 0.3843 time to fit residues: 144.7313 Evaluate side-chains 230 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 226 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 3710 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.0370 chunk 216 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 258 optimal weight: 7.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 GLN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2296 GLN A2752 ASN A3202 ASN A3622 ASN A4381 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098857 restraints weight = 36009.663| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.88 r_work: 0.3057 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23611 Z= 0.155 Angle : 0.540 10.235 32029 Z= 0.270 Chirality : 0.040 0.154 3603 Planarity : 0.004 0.052 4094 Dihedral : 6.833 85.274 3204 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.50 % Favored : 97.36 % Rotamer: Outliers : 2.24 % Allowed : 19.50 % Favored : 78.26 % 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: 1.73 (0.16), residues: 2844 helix: 2.18 (0.13), residues: 1612 sheet: -0.66 (0.36), residues: 232 loop : -0.05 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1701 HIS 0.004 0.001 HIS A4119 PHE 0.018 0.001 PHE A3813 TYR 0.017 0.001 TYR A2748 ARG 0.006 0.000 ARG A1962 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 1325) hydrogen bonds : angle 4.19082 ( 3852) covalent geometry : bond 0.00360 (23611) covalent geometry : angle 0.53970 (32029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 2.796 Fit side-chains revert: symmetry clash REVERT: A 1679 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8098 (ttp80) REVERT: A 1931 ASN cc_start: 0.7956 (p0) cc_final: 0.7405 (p0) REVERT: A 1967 MET cc_start: 0.7903 (mmp) cc_final: 0.7605 (tpt) REVERT: A 2286 LYS cc_start: 0.8395 (mttt) cc_final: 0.8160 (ttmm) REVERT: A 2614 ASP cc_start: 0.8614 (p0) cc_final: 0.8292 (p0) REVERT: A 2632 LEU cc_start: 0.8411 (mm) cc_final: 0.8187 (mm) REVERT: A 2855 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 2881 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: A 2968 THR cc_start: 0.8170 (t) cc_final: 0.7926 (t) REVERT: A 3001 ASP cc_start: 0.8719 (p0) cc_final: 0.8407 (p0) REVERT: A 3169 MET cc_start: 0.8446 (mmt) cc_final: 0.8218 (mmm) REVERT: A 3610 THR cc_start: 0.7149 (m) cc_final: 0.6670 (p) REVERT: A 4018 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.6220 (mmm) REVERT: A 4389 HIS cc_start: 0.7740 (m90) cc_final: 0.7521 (m90) outliers start: 57 outliers final: 27 residues processed: 284 average time/residue: 0.3734 time to fit residues: 166.8481 Evaluate side-chains 256 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2881 TYR Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4084 ILE Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4438 CYS Chi-restraints excluded: chain A residue 4463 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 205 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 262 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099127 restraints weight = 36122.859| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.78 r_work: 0.3087 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23611 Z= 0.128 Angle : 0.502 7.604 32029 Z= 0.250 Chirality : 0.039 0.143 3603 Planarity : 0.004 0.054 4094 Dihedral : 6.622 88.930 3196 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 2.63 % Allowed : 19.22 % Favored : 78.14 % 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: 1.86 (0.16), residues: 2844 helix: 2.35 (0.13), residues: 1607 sheet: -0.69 (0.37), residues: 220 loop : -0.09 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1701 HIS 0.003 0.001 HIS A1817 PHE 0.017 0.001 PHE A3813 TYR 0.016 0.001 TYR A2748 ARG 0.004 0.000 ARG A1962 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1325) hydrogen bonds : angle 4.03348 ( 3852) covalent geometry : bond 0.00293 (23611) covalent geometry : angle 0.50220 (32029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 247 time to evaluate : 2.500 Fit side-chains revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8395 (mmp) REVERT: A 1931 ASN cc_start: 0.7975 (p0) cc_final: 0.7440 (p0) REVERT: A 2127 ILE cc_start: 0.6719 (tt) cc_final: 0.6115 (pt) REVERT: A 2286 LYS cc_start: 0.8410 (mttt) cc_final: 0.8177 (ttmm) REVERT: A 2614 ASP cc_start: 0.8599 (p0) cc_final: 0.8326 (p0) REVERT: A 2855 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8430 (mm) REVERT: A 2867 MET cc_start: 0.5464 (pmm) cc_final: 0.4768 (pmm) REVERT: A 2881 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: A 2968 THR cc_start: 0.8149 (t) cc_final: 0.7925 (t) REVERT: A 3001 ASP cc_start: 0.8668 (p0) cc_final: 0.8416 (p0) REVERT: A 3610 THR cc_start: 0.7270 (m) cc_final: 0.6801 (p) REVERT: A 4018 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.6090 (mmm) outliers start: 67 outliers final: 40 residues processed: 291 average time/residue: 0.3626 time to fit residues: 167.8589 Evaluate side-chains 278 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1892 MET Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2881 TYR Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3198 GLN Chi-restraints excluded: chain A residue 3549 ARG Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3639 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3771 GLU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4042 LEU Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4376 TRP Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 34 optimal weight: 0.4980 chunk 281 optimal weight: 0.0010 chunk 53 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 111 optimal weight: 0.0370 chunk 269 optimal weight: 5.9990 overall best weight: 0.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103128 restraints weight = 36404.278| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.13 r_work: 0.3092 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23611 Z= 0.103 Angle : 0.488 7.681 32029 Z= 0.242 Chirality : 0.039 0.168 3603 Planarity : 0.003 0.057 4094 Dihedral : 6.437 86.441 3196 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.33 % Rotamer: Outliers : 2.59 % Allowed : 19.26 % Favored : 78.14 % 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: 1.98 (0.16), residues: 2844 helix: 2.48 (0.13), residues: 1603 sheet: -0.79 (0.35), residues: 235 loop : -0.03 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1701 HIS 0.004 0.001 HIS A2085 PHE 0.015 0.001 PHE A3813 TYR 0.016 0.001 TYR A3120 ARG 0.004 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1325) hydrogen bonds : angle 3.90049 ( 3852) covalent geometry : bond 0.00224 (23611) covalent geometry : angle 0.48784 (32029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 248 time to evaluate : 2.736 Fit side-chains revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8389 (mmp) REVERT: A 1931 ASN cc_start: 0.7927 (p0) cc_final: 0.7389 (p0) REVERT: A 2286 LYS cc_start: 0.8340 (mttt) cc_final: 0.8118 (ttmm) REVERT: A 2438 GLU cc_start: 0.8537 (tp30) cc_final: 0.8055 (mt-10) REVERT: A 2614 ASP cc_start: 0.8546 (p0) cc_final: 0.8275 (p0) REVERT: A 2632 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8204 (mm) REVERT: A 2867 MET cc_start: 0.5270 (pmm) cc_final: 0.4441 (pmm) REVERT: A 2881 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: A 3001 ASP cc_start: 0.8662 (p0) cc_final: 0.8416 (p0) REVERT: A 3610 THR cc_start: 0.7221 (m) cc_final: 0.6820 (p) REVERT: A 3875 MET cc_start: 0.8422 (ttp) cc_final: 0.8182 (ttt) REVERT: A 4389 HIS cc_start: 0.7676 (m90) cc_final: 0.7385 (m90) outliers start: 66 outliers final: 39 residues processed: 293 average time/residue: 0.3771 time to fit residues: 177.5334 Evaluate side-chains 268 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1892 MET Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2881 TYR Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3198 GLN Chi-restraints excluded: chain A residue 3549 ARG Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3639 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4042 LEU Chi-restraints excluded: chain A residue 4084 ILE Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4270 GLU Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4376 TRP Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 47 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 247 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1922 GLN A2998 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.095887 restraints weight = 36482.602| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.77 r_work: 0.3026 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23611 Z= 0.207 Angle : 0.560 7.957 32029 Z= 0.279 Chirality : 0.042 0.165 3603 Planarity : 0.004 0.050 4094 Dihedral : 6.564 84.212 3196 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 2.87 % Allowed : 19.38 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.16), residues: 2844 helix: 2.31 (0.13), residues: 1607 sheet: -0.84 (0.35), residues: 230 loop : -0.14 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A4478 HIS 0.004 0.001 HIS A3535 PHE 0.021 0.002 PHE A4482 TYR 0.019 0.001 TYR A3516 ARG 0.004 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 1325) hydrogen bonds : angle 4.04568 ( 3852) covalent geometry : bond 0.00499 (23611) covalent geometry : angle 0.56003 (32029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 237 time to evaluate : 2.477 Fit side-chains REVERT: A 1892 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8389 (mmp) REVERT: A 1931 ASN cc_start: 0.8084 (p0) cc_final: 0.7508 (p0) REVERT: A 2286 LYS cc_start: 0.8355 (mttt) cc_final: 0.8144 (ttmm) REVERT: A 2614 ASP cc_start: 0.8631 (p0) cc_final: 0.8416 (p0) REVERT: A 2623 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8110 (m) REVERT: A 2855 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (mm) REVERT: A 2867 MET cc_start: 0.5496 (pmm) cc_final: 0.5284 (pmm) REVERT: A 2881 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: A 3001 ASP cc_start: 0.8620 (p0) cc_final: 0.8407 (p0) REVERT: A 3610 THR cc_start: 0.7297 (m) cc_final: 0.6772 (p) REVERT: A 4018 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6625 (mmm) REVERT: A 4377 MET cc_start: 0.2362 (mtm) cc_final: 0.2117 (mtm) REVERT: A 4389 HIS cc_start: 0.7621 (m90) cc_final: 0.7325 (m90) REVERT: A 4466 HIS cc_start: 0.8089 (m90) cc_final: 0.7806 (m-70) outliers start: 73 outliers final: 52 residues processed: 290 average time/residue: 0.3481 time to fit residues: 162.0083 Evaluate side-chains 275 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1892 MET Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2247 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2454 CYS Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2881 TYR Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3549 ARG Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3639 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4042 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4306 VAL Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4376 TRP Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4532 ASN Chi-restraints excluded: chain A residue 4537 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 127 optimal weight: 0.6980 chunk 256 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 107 optimal weight: 0.0000 chunk 184 optimal weight: 0.9980 chunk 251 optimal weight: 0.7980 chunk 276 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1841 GLN A1973 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099798 restraints weight = 36007.858| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.75 r_work: 0.3081 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 23611 Z= 0.107 Angle : 0.498 8.962 32029 Z= 0.246 Chirality : 0.039 0.149 3603 Planarity : 0.003 0.058 4094 Dihedral : 6.364 82.162 3196 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.36 % Favored : 97.54 % Rotamer: Outliers : 2.04 % Allowed : 20.60 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.98 (0.16), residues: 2844 helix: 2.48 (0.13), residues: 1603 sheet: -0.82 (0.35), residues: 230 loop : -0.05 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4478 HIS 0.003 0.000 HIS A1817 PHE 0.019 0.001 PHE A4482 TYR 0.020 0.001 TYR A3516 ARG 0.004 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 1325) hydrogen bonds : angle 3.87386 ( 3852) covalent geometry : bond 0.00238 (23611) covalent geometry : angle 0.49837 (32029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 2.847 Fit side-chains revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8466 (mmp) REVERT: A 1931 ASN cc_start: 0.7948 (p0) cc_final: 0.7408 (p0) REVERT: A 1973 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7534 (mm-40) REVERT: A 2286 LYS cc_start: 0.8389 (mttt) cc_final: 0.8176 (ttmm) REVERT: A 2310 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8155 (mm-30) REVERT: A 2371 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7953 (m) REVERT: A 2581 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 2848 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7485 (tm-30) REVERT: A 2855 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8324 (mm) REVERT: A 2881 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: A 3001 ASP cc_start: 0.8664 (p0) cc_final: 0.8437 (p0) REVERT: A 3030 MET cc_start: 0.8431 (mmm) cc_final: 0.8096 (mmm) REVERT: A 3610 THR cc_start: 0.7274 (m) cc_final: 0.6827 (p) REVERT: A 3682 ARG cc_start: 0.8647 (mmm160) cc_final: 0.8385 (mmm-85) REVERT: A 3875 MET cc_start: 0.8574 (ttt) cc_final: 0.8256 (ttt) REVERT: A 4018 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.6135 (mmm) REVERT: A 4276 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7910 (mmm-85) REVERT: A 4466 HIS cc_start: 0.8149 (m90) cc_final: 0.7865 (m-70) outliers start: 52 outliers final: 35 residues processed: 284 average time/residue: 0.3701 time to fit residues: 168.1113 Evaluate side-chains 276 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1892 MET Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2881 TYR Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3549 ARG Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3639 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4042 LEU Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4376 TRP Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4537 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 60 optimal weight: 0.6980 chunk 220 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 126 optimal weight: 0.9980 chunk 283 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2849 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096672 restraints weight = 36659.497| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.77 r_work: 0.3056 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 23611 Z= 0.178 Angle : 0.546 8.828 32029 Z= 0.270 Chirality : 0.041 0.165 3603 Planarity : 0.004 0.053 4094 Dihedral : 6.376 85.256 3196 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.94 % Rotamer: Outliers : 2.40 % Allowed : 20.40 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.16), residues: 2844 helix: 2.41 (0.13), residues: 1604 sheet: -0.89 (0.35), residues: 225 loop : -0.12 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A4478 HIS 0.003 0.001 HIS A3151 PHE 0.020 0.001 PHE A1936 TYR 0.018 0.001 TYR A2748 ARG 0.004 0.000 ARG A2844 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 1325) hydrogen bonds : angle 3.95813 ( 3852) covalent geometry : bond 0.00428 (23611) covalent geometry : angle 0.54572 (32029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 2.563 Fit side-chains revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8474 (mmp) REVERT: A 1931 ASN cc_start: 0.8050 (p0) cc_final: 0.7537 (p0) REVERT: A 1973 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7607 (mm-40) REVERT: A 2286 LYS cc_start: 0.8400 (mttt) cc_final: 0.8191 (ttmm) REVERT: A 2623 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8116 (m) REVERT: A 2855 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8364 (mm) REVERT: A 2881 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: A 3001 ASP cc_start: 0.8638 (p0) cc_final: 0.8412 (p0) REVERT: A 3169 MET cc_start: 0.8274 (mmt) cc_final: 0.8063 (mmm) REVERT: A 3610 THR cc_start: 0.7391 (m) cc_final: 0.6871 (p) REVERT: A 3682 ARG cc_start: 0.8699 (mmm160) cc_final: 0.8404 (mmm-85) REVERT: A 4018 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.6564 (mmm) REVERT: A 4247 MET cc_start: 0.8955 (mtm) cc_final: 0.8741 (mtp) REVERT: A 4389 HIS cc_start: 0.7602 (m90) cc_final: 0.7378 (m90) REVERT: A 4433 ASP cc_start: 0.6865 (t0) cc_final: 0.6583 (t0) REVERT: A 4466 HIS cc_start: 0.8108 (m90) cc_final: 0.7844 (m-70) outliers start: 61 outliers final: 45 residues processed: 282 average time/residue: 0.3650 time to fit residues: 165.2272 Evaluate side-chains 273 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1892 MET Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2171 HIS Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2881 TYR Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3549 ARG Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3639 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4042 LEU Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4376 TRP Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4532 ASN Chi-restraints excluded: chain A residue 4537 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 221 optimal weight: 0.0770 chunk 242 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 269 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.137658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098209 restraints weight = 36185.430| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.90 r_work: 0.3061 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23611 Z= 0.115 Angle : 0.514 10.341 32029 Z= 0.254 Chirality : 0.039 0.159 3603 Planarity : 0.003 0.057 4094 Dihedral : 6.215 87.983 3196 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.53 % Favored : 97.36 % Rotamer: Outliers : 2.40 % Allowed : 20.68 % Favored : 76.93 % 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: 1.97 (0.16), residues: 2844 helix: 2.49 (0.13), residues: 1604 sheet: -0.79 (0.35), residues: 214 loop : -0.11 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A4478 HIS 0.003 0.000 HIS A1985 PHE 0.019 0.001 PHE A1936 TYR 0.018 0.001 TYR A3516 ARG 0.004 0.000 ARG A2844 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 1325) hydrogen bonds : angle 3.87312 ( 3852) covalent geometry : bond 0.00262 (23611) covalent geometry : angle 0.51404 (32029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 2.525 Fit side-chains revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8529 (mmp) REVERT: A 1931 ASN cc_start: 0.7970 (p0) cc_final: 0.7446 (p0) REVERT: A 1973 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7624 (mm-40) REVERT: A 2286 LYS cc_start: 0.8454 (mttt) cc_final: 0.8234 (ttmm) REVERT: A 2371 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8040 (m) REVERT: A 2623 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8099 (m) REVERT: A 2855 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8401 (mm) REVERT: A 2881 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: A 3001 ASP cc_start: 0.8694 (p0) cc_final: 0.8447 (p0) REVERT: A 3030 MET cc_start: 0.8465 (mmm) cc_final: 0.8128 (mmm) REVERT: A 3169 MET cc_start: 0.8226 (mmt) cc_final: 0.8011 (mmm) REVERT: A 3610 THR cc_start: 0.7375 (m) cc_final: 0.6885 (p) REVERT: A 3682 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8417 (mmm-85) REVERT: A 4018 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.6234 (mmm) REVERT: A 4389 HIS cc_start: 0.7585 (m90) cc_final: 0.7335 (m90) REVERT: A 4466 HIS cc_start: 0.8131 (m90) cc_final: 0.7887 (m-70) outliers start: 61 outliers final: 49 residues processed: 289 average time/residue: 0.3578 time to fit residues: 165.4804 Evaluate side-chains 291 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 236 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1892 MET Chi-restraints excluded: chain A residue 2005 GLN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2881 TYR Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3549 ARG Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3639 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4042 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4270 GLU Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4306 VAL Chi-restraints excluded: chain A residue 4376 TRP Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4438 CYS Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4537 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 20.0000 chunk 279 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 274 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097412 restraints weight = 36260.484| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.91 r_work: 0.3056 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23611 Z= 0.129 Angle : 0.523 11.120 32029 Z= 0.257 Chirality : 0.039 0.155 3603 Planarity : 0.003 0.056 4094 Dihedral : 6.039 77.792 3196 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 2.20 % Allowed : 20.87 % Favored : 76.93 % 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: 1.97 (0.16), residues: 2844 helix: 2.48 (0.13), residues: 1605 sheet: -0.75 (0.35), residues: 214 loop : -0.12 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4478 HIS 0.004 0.001 HIS A1985 PHE 0.021 0.001 PHE A1936 TYR 0.020 0.001 TYR A2748 ARG 0.004 0.000 ARG A2844 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 1325) hydrogen bonds : angle 3.86789 ( 3852) covalent geometry : bond 0.00301 (23611) covalent geometry : angle 0.52276 (32029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8508 (mmp) REVERT: A 1931 ASN cc_start: 0.7980 (p0) cc_final: 0.7453 (p0) REVERT: A 1973 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7625 (mm-40) REVERT: A 2286 LYS cc_start: 0.8405 (mttt) cc_final: 0.8191 (ttmm) REVERT: A 2371 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8035 (m) REVERT: A 2623 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8112 (m) REVERT: A 2855 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8370 (mm) REVERT: A 2881 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: A 3001 ASP cc_start: 0.8689 (p0) cc_final: 0.8441 (p0) REVERT: A 3030 MET cc_start: 0.8482 (mmm) cc_final: 0.8143 (mmm) REVERT: A 3169 MET cc_start: 0.8250 (mmt) cc_final: 0.8048 (mmm) REVERT: A 3610 THR cc_start: 0.7363 (m) cc_final: 0.6869 (p) REVERT: A 3682 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8409 (mmm-85) REVERT: A 4018 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.6409 (mmm) REVERT: A 4276 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7820 (mmm-85) REVERT: A 4466 HIS cc_start: 0.8165 (m90) cc_final: 0.7945 (m-70) outliers start: 56 outliers final: 48 residues processed: 282 average time/residue: 0.3881 time to fit residues: 176.7753 Evaluate side-chains 290 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1892 MET Chi-restraints excluded: chain A residue 2005 GLN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2881 TYR Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3549 ARG Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3639 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4042 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4270 GLU Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4376 TRP Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4438 CYS Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4537 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 207 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 179 optimal weight: 3.9990 chunk 158 optimal weight: 0.0980 chunk 113 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097231 restraints weight = 36365.236| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.90 r_work: 0.3050 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23611 Z= 0.139 Angle : 0.529 11.363 32029 Z= 0.261 Chirality : 0.040 0.155 3603 Planarity : 0.003 0.055 4094 Dihedral : 5.980 76.974 3196 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 2.20 % Allowed : 21.11 % Favored : 76.69 % 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: 1.96 (0.16), residues: 2844 helix: 2.48 (0.13), residues: 1603 sheet: -0.89 (0.36), residues: 201 loop : -0.09 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4478 HIS 0.004 0.001 HIS A1985 PHE 0.017 0.001 PHE A3813 TYR 0.016 0.001 TYR A3120 ARG 0.004 0.000 ARG A2844 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 1325) hydrogen bonds : angle 3.87954 ( 3852) covalent geometry : bond 0.00328 (23611) covalent geometry : angle 0.52907 (32029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1892 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8522 (mmp) REVERT: A 1931 ASN cc_start: 0.7987 (p0) cc_final: 0.7460 (p0) REVERT: A 1973 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7644 (mm-40) REVERT: A 2286 LYS cc_start: 0.8391 (mttt) cc_final: 0.8183 (ttmm) REVERT: A 2371 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8047 (m) REVERT: A 2623 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8118 (m) REVERT: A 2855 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8356 (mm) REVERT: A 2881 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: A 3001 ASP cc_start: 0.8693 (p0) cc_final: 0.8458 (p0) REVERT: A 3030 MET cc_start: 0.8469 (mmm) cc_final: 0.8132 (mmm) REVERT: A 3610 THR cc_start: 0.7361 (m) cc_final: 0.6854 (p) REVERT: A 3682 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8384 (mmm-85) REVERT: A 4018 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.6460 (mmm) REVERT: A 4276 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7789 (mmm-85) REVERT: A 4466 HIS cc_start: 0.8153 (m90) cc_final: 0.7945 (m-70) outliers start: 56 outliers final: 50 residues processed: 280 average time/residue: 0.4035 time to fit residues: 183.5524 Evaluate side-chains 289 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1510 SER Chi-restraints excluded: chain A residue 1632 VAL Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1854 LEU Chi-restraints excluded: chain A residue 1892 MET Chi-restraints excluded: chain A residue 2005 GLN Chi-restraints excluded: chain A residue 2031 ASN Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2204 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2534 ILE Chi-restraints excluded: chain A residue 2605 LEU Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2881 TYR Chi-restraints excluded: chain A residue 2905 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3549 ARG Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3629 PHE Chi-restraints excluded: chain A residue 3639 GLU Chi-restraints excluded: chain A residue 3677 ILE Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3961 LEU Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4042 LEU Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4270 GLU Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4306 VAL Chi-restraints excluded: chain A residue 4376 TRP Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4438 CYS Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4537 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 70 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.134438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094847 restraints weight = 36411.151| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.89 r_work: 0.3018 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23611 Z= 0.189 Angle : 0.569 11.263 32029 Z= 0.282 Chirality : 0.041 0.154 3603 Planarity : 0.004 0.051 4094 Dihedral : 6.085 80.702 3196 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.84 % Rotamer: Outliers : 2.36 % Allowed : 20.95 % Favored : 76.69 % 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: 1.81 (0.16), residues: 2844 helix: 2.36 (0.13), residues: 1603 sheet: -1.11 (0.35), residues: 210 loop : -0.12 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A4478 HIS 0.007 0.001 HIS A1985 PHE 0.020 0.002 PHE A3813 TYR 0.020 0.001 TYR A4252 ARG 0.005 0.000 ARG A2844 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 1325) hydrogen bonds : angle 3.99875 ( 3852) covalent geometry : bond 0.00453 (23611) covalent geometry : angle 0.56925 (32029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13236.50 seconds wall clock time: 230 minutes 15.47 seconds (13815.47 seconds total)