Starting phenix.real_space_refine on Thu Jun 19 07:12:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm4_44687/06_2025/9bm4_44687.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm4_44687/06_2025/9bm4_44687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bm4_44687/06_2025/9bm4_44687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm4_44687/06_2025/9bm4_44687.map" model { file = "/net/cci-nas-00/data/ceres_data/9bm4_44687/06_2025/9bm4_44687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm4_44687/06_2025/9bm4_44687.cif" } resolution = 3.48 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= 0.021 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 111 5.16 5 C 13851 2.51 5 N 3763 2.21 5 O 4065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 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: 21801 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2701, 21684 Classifications: {'peptide': 2701} Link IDs: {'PTRANS': 126, 'TRANS': 2574} Chain breaks: 6 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: 14.19, per 1000 atoms: 0.65 Number of scatterers: 21801 At special positions: 0 Unit cell: (148.928, 157.248, 123.968, 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 111 16.00 P 10 15.00 Mg 1 11.99 O 4065 8.00 N 3763 7.00 C 13851 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: 5.58 Conformation dependent library (CDL) restraints added in 2.7 seconds 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5134 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 20 sheets defined 61.2% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 1626 through 1632 removed outlier: 3.588A pdb=" N PHE A1629 " --> pdb=" O PHE A1626 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A1632 " --> pdb=" O PHE A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1649 Processing helix chain 'A' and resid 1650 through 1658 Processing helix chain 'A' and resid 1697 through 1728 Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.742A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1938 through 1952 Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1986 removed outlier: 3.639A pdb=" N SER A1986 " --> pdb=" O LEU A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.506A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2133 through 2146 Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 3.581A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2320 removed outlier: 3.937A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.556A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) 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 2428 removed outlier: 3.745A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.649A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.625A pdb=" N SER A2503 " --> pdb=" O LEU A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2548 through 2552 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.664A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.747A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.180A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2764 Proline residue: A2760 - end of helix removed outlier: 5.155A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.844A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.504A 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 removed outlier: 3.580A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.881A 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 3062 Processing helix chain 'A' and resid 3082 through 3088 removed outlier: 3.527A pdb=" N PHE A3086 " --> pdb=" O SER A3082 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A3088 " --> pdb=" O ALA A3084 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.654A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3516 removed outlier: 4.774A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 4.016A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.982A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 3.578A pdb=" N CYS A3693 " --> pdb=" O PRO A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3729 Processing helix chain 'A' and resid 3729 through 3735 removed outlier: 4.363A pdb=" N GLN A3735 " --> pdb=" O LEU A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3738 through 3754 removed outlier: 3.522A pdb=" N LEU A3742 " --> pdb=" O PHE A3738 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN A3754 " --> pdb=" O LEU A3750 " (cutoff:3.500A) Processing helix chain 'A' and resid 3764 through 3767 removed outlier: 3.575A pdb=" N ILE A3767 " --> pdb=" O ASP A3764 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3764 through 3767' Processing helix chain 'A' and resid 3768 through 3790 removed outlier: 3.601A pdb=" N ASN A3772 " --> pdb=" O THR A3768 " (cutoff:3.500A) Processing helix chain 'A' and resid 3793 through 3818 removed outlier: 4.041A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.562A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3872 Processing helix chain 'A' and resid 3873 through 3875 No H-bonds generated for 'chain 'A' and resid 3873 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.129A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.574A 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 3963 Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.106A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.793A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4033 Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.610A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 3.974A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4116 Processing helix chain 'A' and resid 4135 through 4142 removed outlier: 3.659A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.993A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS A4170 " --> pdb=" O VAL A4166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4165 through 4170' Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.321A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.572A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.713A pdb=" N PHE A4278 " --> pdb=" O THR A4275 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.598A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4321 Processing helix chain 'A' and resid 4325 through 4347 removed outlier: 4.476A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A4347 " --> pdb=" O MET A4343 " (cutoff:3.500A) Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4407 Processing helix chain 'A' and resid 4407 through 4440 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4500 through 4505 Processing helix chain 'A' and resid 4516 through 4532 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 3.760A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1902 through 1905 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1929 removed outlier: 6.539A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA6, first strand: chain 'A' and resid 2219 through 2220 removed outlier: 6.716A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2222 through 2223 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 2617 through 2620 removed outlier: 5.975A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 4.356A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.530A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.581A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3612 removed outlier: 6.595A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3654 through 3656 removed outlier: 3.553A pdb=" N ARG A3654 " --> pdb=" O LEU A3661 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.320A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510 Processing sheet with id=AC1, first strand: chain 'A' and resid 4583 through 4584 removed outlier: 8.349A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4570 1241 hydrogen bonds defined for protein. 3633 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: 13.36 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7047 1.34 - 1.46: 2951 1.46 - 1.57: 12073 1.57 - 1.69: 16 1.69 - 1.81: 185 Bond restraints: 22272 Sorted by residual: bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" N VAL A3756 " pdb=" CA VAL A3756 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.68e+00 bond pdb=" N ILE A3760 " pdb=" CA ILE A3760 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.50e+00 bond pdb=" N LEU A2324 " pdb=" CA LEU A2324 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.12e+00 ... (remaining 22267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 29940 2.80 - 5.60: 240 5.60 - 8.39: 25 8.39 - 11.19: 11 11.19 - 13.99: 2 Bond angle restraints: 30218 Sorted by residual: angle pdb=" PB ATP A4703 " pdb=" O3B ATP A4703 " pdb=" PG ATP A4703 " ideal model delta sigma weight residual 139.87 129.71 10.16 1.00e+00 1.00e+00 1.03e+02 angle pdb=" PA ATP A4703 " pdb=" O3A ATP A4703 " pdb=" PB ATP A4703 " ideal model delta sigma weight residual 136.83 127.27 9.56 1.00e+00 1.00e+00 9.14e+01 angle pdb=" N GLU A3755 " pdb=" CA GLU A3755 " pdb=" C GLU A3755 " ideal model delta sigma weight residual 113.21 108.49 4.72 1.15e+00 7.56e-01 1.68e+01 angle pdb=" CA LEU A1766 " pdb=" CB LEU A1766 " pdb=" CG LEU A1766 " ideal model delta sigma weight residual 116.30 130.29 -13.99 3.50e+00 8.16e-02 1.60e+01 angle pdb=" CA LEU A4451 " pdb=" CB LEU A4451 " pdb=" CG LEU A4451 " ideal model delta sigma weight residual 116.30 129.01 -12.71 3.50e+00 8.16e-02 1.32e+01 ... (remaining 30213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.65: 12389 25.65 - 51.30: 966 51.30 - 76.95: 143 76.95 - 102.60: 18 102.60 - 128.25: 2 Dihedral angle restraints: 13518 sinusoidal: 5617 harmonic: 7901 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 68.25 -128.25 1 2.00e+01 2.50e-03 3.89e+01 dihedral pdb=" CA PHE A1926 " pdb=" C PHE A1926 " pdb=" N VAL A1927 " pdb=" CA VAL A1927 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+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 48.53 -108.53 1 2.00e+01 2.50e-03 3.16e+01 ... (remaining 13515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3160 0.079 - 0.157: 238 0.157 - 0.236: 3 0.236 - 0.315: 0 0.315 - 0.394: 1 Chirality restraints: 3402 Sorted by residual: chirality pdb=" CG LEU A1766 " pdb=" CB LEU A1766 " pdb=" CD1 LEU A1766 " pdb=" CD2 LEU A1766 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA ILE A3760 " pdb=" N ILE A3760 " pdb=" C ILE A3760 " pdb=" CB ILE A3760 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA VAL A3756 " pdb=" N VAL A3756 " pdb=" C VAL A3756 " pdb=" CB VAL A3756 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 3399 not shown) Planarity restraints: 3869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A3136 " 0.077 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO A3137 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO A3137 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A3137 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A3122 " 0.047 5.00e-02 4.00e+02 7.21e-02 8.33e+00 pdb=" N PRO A3123 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A3123 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A3123 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A3629 " 0.015 2.00e-02 2.50e+03 1.89e-02 6.23e+00 pdb=" CG PHE A3629 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A3629 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A3629 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A3629 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A3629 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A3629 " -0.000 2.00e-02 2.50e+03 ... (remaining 3866 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 169 2.58 - 3.16: 18565 3.16 - 3.74: 36146 3.74 - 4.32: 46941 4.32 - 4.90: 78039 Nonbonded interactions: 179860 Sorted by model distance: nonbonded pdb=" OG1 THR A2602 " pdb="MG MG A4705 " model vdw 1.996 2.170 nonbonded pdb=" OG SER A2099 " pdb=" OG SER A2140 " model vdw 2.166 3.040 nonbonded pdb=" OG SER A2231 " pdb=" OE2 GLU A2344 " model vdw 2.199 3.040 nonbonded pdb=" OE1 GLU A3100 " pdb=" OH TYR A3130 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR A1688 " pdb=" OE2 GLU A1708 " model vdw 2.208 3.040 ... (remaining 179855 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: 4.870 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: 1.010 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 58.220 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 22272 Z= 0.178 Angle : 0.658 13.988 30218 Z= 0.349 Chirality : 0.041 0.394 3402 Planarity : 0.005 0.117 3869 Dihedral : 17.574 128.252 8384 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.50 % Allowed : 24.08 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.16), residues: 2687 helix: 1.78 (0.13), residues: 1495 sheet: -0.70 (0.35), residues: 228 loop : 0.22 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4376 HIS 0.016 0.001 HIS A3852 PHE 0.044 0.002 PHE A3629 TYR 0.029 0.002 TYR A3103 ARG 0.009 0.000 ARG A1843 Details of bonding type rmsd hydrogen bonds : bond 0.13663 ( 1241) hydrogen bonds : angle 5.84090 ( 3633) covalent geometry : bond 0.00355 (22272) covalent geometry : angle 0.65816 (30218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 276 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6249 (pmm) REVERT: A 1938 PHE cc_start: 0.7539 (t80) cc_final: 0.7149 (m-80) REVERT: A 2792 TYR cc_start: 0.7452 (m-80) cc_final: 0.7249 (m-80) REVERT: A 2994 MET cc_start: 0.8248 (tpt) cc_final: 0.7856 (tpt) REVERT: A 4451 LEU cc_start: 0.8158 (tt) cc_final: 0.7932 (tt) outliers start: 12 outliers final: 7 residues processed: 281 average time/residue: 0.3100 time to fit residues: 142.7765 Evaluate side-chains 265 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 2987 ASN Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3521 ASP Chi-restraints excluded: chain A residue 4109 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 0.9980 chunk 204 optimal weight: 0.4980 chunk 113 optimal weight: 0.1980 chunk 69 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 211 optimal weight: 0.0040 chunk 81 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 245 optimal weight: 8.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2416 GLN A2875 ASN A2928 GLN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN A3631 ASN A3838 ASN A4029 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4573 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.132479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.103418 restraints weight = 43919.003| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.17 r_work: 0.3292 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22272 Z= 0.121 Angle : 0.552 11.444 30218 Z= 0.278 Chirality : 0.040 0.293 3402 Planarity : 0.005 0.080 3869 Dihedral : 7.420 95.734 3040 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.75 % Allowed : 21.50 % Favored : 75.75 % 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: 1.58 (0.16), residues: 2687 helix: 1.90 (0.13), residues: 1515 sheet: -0.61 (0.33), residues: 246 loop : 0.19 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2234 HIS 0.004 0.001 HIS A3535 PHE 0.027 0.001 PHE A2682 TYR 0.021 0.001 TYR A1745 ARG 0.017 0.000 ARG A3628 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 1241) hydrogen bonds : angle 4.72991 ( 3633) covalent geometry : bond 0.00259 (22272) covalent geometry : angle 0.55161 (30218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5921 (ptp) REVERT: A 1843 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.6671 (mtm-85) REVERT: A 1926 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: A 1967 MET cc_start: 0.8498 (mmm) cc_final: 0.8027 (mmt) REVERT: A 2232 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7427 (mmt) REVERT: A 2816 LEU cc_start: 0.8663 (tt) cc_final: 0.7833 (mp) REVERT: A 2923 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8370 (t0) REVERT: A 3008 MET cc_start: 0.9078 (mmm) cc_final: 0.8856 (mmm) REVERT: A 3485 GLU cc_start: 0.3547 (OUTLIER) cc_final: 0.3241 (tm-30) REVERT: A 3501 SER cc_start: 0.8284 (t) cc_final: 0.8024 (p) REVERT: A 3725 ASP cc_start: 0.7210 (t70) cc_final: 0.6998 (t70) REVERT: A 3791 MET cc_start: 0.7210 (pmm) cc_final: 0.6743 (mmm) REVERT: A 4062 GLN cc_start: 0.5728 (mm-40) cc_final: 0.5331 (mm110) REVERT: A 4116 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6861 (mp) REVERT: A 4451 LEU cc_start: 0.8130 (tt) cc_final: 0.7866 (tt) REVERT: A 4454 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7650 (tp30) outliers start: 66 outliers final: 25 residues processed: 335 average time/residue: 0.3630 time to fit residues: 201.0839 Evaluate side-chains 286 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1926 PHE Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2923 ASP Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3485 GLU Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4034 GLU Chi-restraints excluded: chain A residue 4095 MET Chi-restraints excluded: chain A residue 4116 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4459 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 121 optimal weight: 7.9990 chunk 168 optimal weight: 0.1980 chunk 4 optimal weight: 0.0010 chunk 200 optimal weight: 0.0470 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A3852 HIS A4526 GLN A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.133822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.103630 restraints weight = 44761.598| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.41 r_work: 0.3330 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22272 Z= 0.108 Angle : 0.527 10.963 30218 Z= 0.263 Chirality : 0.039 0.272 3402 Planarity : 0.004 0.047 3869 Dihedral : 6.879 79.228 3028 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.75 % Allowed : 21.33 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.16), residues: 2687 helix: 1.96 (0.13), residues: 1517 sheet: -0.57 (0.33), residues: 246 loop : 0.15 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.006 0.001 HIS A3852 PHE 0.022 0.001 PHE A2682 TYR 0.020 0.001 TYR A1745 ARG 0.004 0.000 ARG A3628 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 1241) hydrogen bonds : angle 4.47711 ( 3633) covalent geometry : bond 0.00230 (22272) covalent geometry : angle 0.52685 (30218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.6095 (ptp) REVERT: A 1766 LEU cc_start: 0.8130 (mm) cc_final: 0.7876 (mm) REVERT: A 1843 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.6655 (mtm-85) REVERT: A 1926 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: A 1938 PHE cc_start: 0.7478 (t80) cc_final: 0.6765 (m-80) REVERT: A 2792 TYR cc_start: 0.7685 (m-80) cc_final: 0.7388 (m-80) REVERT: A 2816 LEU cc_start: 0.8608 (tt) cc_final: 0.7880 (mp) REVERT: A 2867 MET cc_start: 0.7095 (ttt) cc_final: 0.6869 (ppp) REVERT: A 2934 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8188 (tp) REVERT: A 3501 SER cc_start: 0.8280 (t) cc_final: 0.8040 (p) REVERT: A 3731 LEU cc_start: 0.3427 (OUTLIER) cc_final: 0.2942 (pp) REVERT: A 3791 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6637 (mmm) REVERT: A 4062 GLN cc_start: 0.5686 (mm-40) cc_final: 0.5242 (mm110) REVERT: A 4454 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7656 (tp30) REVERT: A 4516 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7436 (m) outliers start: 66 outliers final: 32 residues processed: 337 average time/residue: 0.3193 time to fit residues: 177.2677 Evaluate side-chains 301 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1657 MET Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1926 PHE Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2366 GLU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4034 GLU Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4498 SER Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 20 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2928 GLN A3087 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3622 ASN A3631 ASN A3838 ASN A4029 HIS A4573 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.130219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.101362 restraints weight = 44572.490| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.14 r_work: 0.3249 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22272 Z= 0.152 Angle : 0.540 10.815 30218 Z= 0.271 Chirality : 0.040 0.198 3402 Planarity : 0.004 0.050 3869 Dihedral : 6.796 88.830 3028 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.21 % Allowed : 21.33 % Favored : 75.46 % 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: 1.64 (0.16), residues: 2687 helix: 1.99 (0.13), residues: 1516 sheet: -0.56 (0.33), residues: 249 loop : 0.16 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.003 0.001 HIS A4187 PHE 0.018 0.002 PHE A2682 TYR 0.023 0.002 TYR A4636 ARG 0.008 0.000 ARG A2507 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1241) hydrogen bonds : angle 4.39343 ( 3633) covalent geometry : bond 0.00357 (22272) covalent geometry : angle 0.53987 (30218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 277 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1766 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7995 (mm) REVERT: A 1896 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8584 (mm) REVERT: A 1926 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: A 1967 MET cc_start: 0.8572 (mmm) cc_final: 0.7894 (mmt) REVERT: A 2012 MET cc_start: 0.7754 (tpt) cc_final: 0.7479 (tpt) REVERT: A 2271 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7535 (m-40) REVERT: A 2676 THR cc_start: 0.9001 (m) cc_final: 0.8414 (p) REVERT: A 2934 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8228 (tp) REVERT: A 2995 ASP cc_start: 0.7828 (t0) cc_final: 0.7613 (t0) REVERT: A 3217 GLU cc_start: -0.0175 (OUTLIER) cc_final: -0.2192 (tp30) REVERT: A 3501 SER cc_start: 0.8266 (t) cc_final: 0.8001 (p) REVERT: A 3731 LEU cc_start: 0.3315 (OUTLIER) cc_final: 0.2644 (pp) REVERT: A 4062 GLN cc_start: 0.5768 (mm-40) cc_final: 0.5297 (mm110) REVERT: A 4158 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 4451 LEU cc_start: 0.8145 (tt) cc_final: 0.7861 (tt) REVERT: A 4454 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7781 (tp30) REVERT: A 4516 VAL cc_start: 0.7697 (OUTLIER) cc_final: 0.7445 (m) outliers start: 77 outliers final: 45 residues processed: 328 average time/residue: 0.3200 time to fit residues: 174.5492 Evaluate side-chains 301 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1685 MET Chi-restraints excluded: chain A residue 1738 TYR Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1926 PHE Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2271 ASN Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2366 GLU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4034 GLU Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4498 SER Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 133 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 266 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.0470 chunk 155 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 257 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2875 ASN A3087 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4029 HIS A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.131987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101575 restraints weight = 44335.278| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.32 r_work: 0.3236 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22272 Z= 0.110 Angle : 0.514 10.695 30218 Z= 0.256 Chirality : 0.039 0.175 3402 Planarity : 0.004 0.045 3869 Dihedral : 6.544 84.582 3025 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.96 % Allowed : 22.04 % Favored : 75.00 % 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: 1.70 (0.17), residues: 2687 helix: 2.04 (0.13), residues: 1521 sheet: -0.51 (0.33), residues: 248 loop : 0.16 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.002 0.000 HIS A2588 PHE 0.016 0.001 PHE A2682 TYR 0.016 0.001 TYR A1745 ARG 0.006 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 1241) hydrogen bonds : angle 4.25858 ( 3633) covalent geometry : bond 0.00244 (22272) covalent geometry : angle 0.51449 (30218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6666 (ptp) cc_final: 0.6242 (mpp) REVERT: A 1766 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7949 (mm) REVERT: A 1861 MET cc_start: 0.5831 (ttt) cc_final: 0.5614 (ttt) REVERT: A 1926 PHE cc_start: 0.7668 (t80) cc_final: 0.7357 (m-80) REVERT: A 1938 PHE cc_start: 0.7469 (t80) cc_final: 0.6710 (m-80) REVERT: A 2012 MET cc_start: 0.7730 (tpt) cc_final: 0.7466 (tpt) REVERT: A 2271 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.7551 (m-40) REVERT: A 2676 THR cc_start: 0.8982 (m) cc_final: 0.8386 (p) REVERT: A 2934 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8091 (tp) REVERT: A 3169 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7060 (mpp) REVERT: A 3217 GLU cc_start: -0.0430 (OUTLIER) cc_final: -0.2399 (tp30) REVERT: A 3501 SER cc_start: 0.8314 (t) cc_final: 0.8039 (p) REVERT: A 3731 LEU cc_start: 0.3336 (OUTLIER) cc_final: 0.2742 (pp) REVERT: A 4062 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5310 (mm110) REVERT: A 4158 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8739 (mm) REVERT: A 4454 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7687 (tp30) REVERT: A 4516 VAL cc_start: 0.7665 (OUTLIER) cc_final: 0.7419 (m) outliers start: 71 outliers final: 42 residues processed: 314 average time/residue: 0.2941 time to fit residues: 154.3904 Evaluate side-chains 298 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1685 MET Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 2271 ASN Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2366 GLU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4034 GLU Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 172 optimal weight: 0.0980 chunk 83 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2376 ASN A3087 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4029 HIS A4573 ASN A4597 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.131158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100816 restraints weight = 44246.128| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.30 r_work: 0.3220 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22272 Z= 0.124 Angle : 0.531 14.904 30218 Z= 0.261 Chirality : 0.039 0.176 3402 Planarity : 0.004 0.052 3869 Dihedral : 6.354 81.197 3023 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.83 % Allowed : 22.67 % Favored : 74.50 % 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: 1.75 (0.16), residues: 2687 helix: 2.08 (0.13), residues: 1516 sheet: -0.44 (0.33), residues: 249 loop : 0.16 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.003 0.001 HIS A2588 PHE 0.014 0.001 PHE A1836 TYR 0.021 0.001 TYR A4636 ARG 0.006 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 1241) hydrogen bonds : angle 4.21012 ( 3633) covalent geometry : bond 0.00285 (22272) covalent geometry : angle 0.53075 (30218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6455 (ptp) cc_final: 0.6131 (mpp) REVERT: A 1766 LEU cc_start: 0.8264 (mm) cc_final: 0.7924 (mm) REVERT: A 1861 MET cc_start: 0.6300 (ttt) cc_final: 0.5924 (ttt) REVERT: A 1896 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8581 (mm) REVERT: A 1926 PHE cc_start: 0.7715 (t80) cc_final: 0.7467 (m-80) REVERT: A 1938 PHE cc_start: 0.7517 (t80) cc_final: 0.6743 (m-80) REVERT: A 2262 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6712 (t70) REVERT: A 2271 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7605 (m-40) REVERT: A 2676 THR cc_start: 0.8984 (m) cc_final: 0.8393 (p) REVERT: A 2934 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8118 (tp) REVERT: A 3161 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8204 (tt) REVERT: A 3169 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7223 (mpp) REVERT: A 3217 GLU cc_start: -0.0442 (OUTLIER) cc_final: -0.2482 (tp30) REVERT: A 3501 SER cc_start: 0.8315 (t) cc_final: 0.8046 (p) REVERT: A 3731 LEU cc_start: 0.3386 (OUTLIER) cc_final: 0.2774 (pp) REVERT: A 4062 GLN cc_start: 0.5775 (mm-40) cc_final: 0.5293 (mm110) REVERT: A 4158 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8758 (mm) REVERT: A 4454 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7657 (tp30) REVERT: A 4516 VAL cc_start: 0.7665 (OUTLIER) cc_final: 0.7409 (m) outliers start: 68 outliers final: 46 residues processed: 313 average time/residue: 0.3005 time to fit residues: 156.6258 Evaluate side-chains 311 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1685 MET Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 2262 ASP Chi-restraints excluded: chain A residue 2271 ASN Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2366 GLU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4034 GLU Chi-restraints excluded: chain A residue 4094 VAL Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4498 SER Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 96 optimal weight: 0.0020 chunk 103 optimal weight: 4.9990 chunk 118 optimal weight: 0.0070 chunk 256 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 227 optimal weight: 0.7980 overall best weight: 1.1610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3711 GLN A3838 ASN A4029 HIS A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101317 restraints weight = 44276.571| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.33 r_work: 0.3218 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22272 Z= 0.129 Angle : 0.529 14.033 30218 Z= 0.261 Chirality : 0.039 0.167 3402 Planarity : 0.004 0.044 3869 Dihedral : 6.234 80.793 3023 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.21 % Allowed : 22.50 % Favored : 74.29 % 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: 2687 helix: 2.09 (0.13), residues: 1514 sheet: -0.38 (0.33), residues: 248 loop : 0.19 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.003 0.001 HIS A3047 PHE 0.015 0.001 PHE A1836 TYR 0.021 0.001 TYR A4636 ARG 0.005 0.000 ARG A4263 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1241) hydrogen bonds : angle 4.18492 ( 3633) covalent geometry : bond 0.00300 (22272) covalent geometry : angle 0.52931 (30218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 271 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6494 (ptp) cc_final: 0.6198 (mpp) REVERT: A 1766 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8041 (mm) REVERT: A 1861 MET cc_start: 0.6552 (ttt) cc_final: 0.6212 (ttt) REVERT: A 1896 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8600 (mm) REVERT: A 1938 PHE cc_start: 0.7433 (t80) cc_final: 0.6704 (m-80) REVERT: A 2262 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6644 (t70) REVERT: A 2271 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7534 (m-40) REVERT: A 2676 THR cc_start: 0.9015 (m) cc_final: 0.8432 (p) REVERT: A 2904 GLU cc_start: 0.8097 (tp30) cc_final: 0.7835 (tp30) REVERT: A 2995 ASP cc_start: 0.7551 (m-30) cc_final: 0.7063 (t0) REVERT: A 3068 MET cc_start: 0.8152 (ptm) cc_final: 0.7722 (ptp) REVERT: A 3161 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 3169 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7416 (mpp) REVERT: A 3217 GLU cc_start: -0.0464 (OUTLIER) cc_final: -0.2522 (tp30) REVERT: A 3501 SER cc_start: 0.8326 (t) cc_final: 0.8056 (p) REVERT: A 3662 ILE cc_start: 0.7246 (mm) cc_final: 0.6792 (mm) REVERT: A 3731 LEU cc_start: 0.3408 (OUTLIER) cc_final: 0.2790 (pp) REVERT: A 4158 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8781 (mm) REVERT: A 4213 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.8190 (ttm-80) REVERT: A 4454 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7627 (tp30) REVERT: A 4516 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7429 (m) outliers start: 77 outliers final: 50 residues processed: 322 average time/residue: 0.3066 time to fit residues: 163.7261 Evaluate side-chains 319 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1738 TYR Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 2262 ASP Chi-restraints excluded: chain A residue 2271 ASN Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2366 GLU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4034 GLU Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4498 SER Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 241 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 264 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1653 HIS A3087 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4029 HIS A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.130946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.100500 restraints weight = 44512.180| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.31 r_work: 0.3216 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22272 Z= 0.121 Angle : 0.540 15.017 30218 Z= 0.263 Chirality : 0.039 0.154 3402 Planarity : 0.004 0.055 3869 Dihedral : 6.164 81.214 3023 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.92 % Allowed : 22.75 % Favored : 74.33 % 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 (0.17), residues: 2687 helix: 2.13 (0.13), residues: 1513 sheet: -0.38 (0.33), residues: 248 loop : 0.19 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.003 0.000 HIS A2588 PHE 0.014 0.001 PHE A1836 TYR 0.030 0.001 TYR A4636 ARG 0.004 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1241) hydrogen bonds : angle 4.17026 ( 3633) covalent geometry : bond 0.00277 (22272) covalent geometry : angle 0.54008 (30218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 271 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6520 (ptp) cc_final: 0.6272 (mpp) REVERT: A 1857 LEU cc_start: 0.6470 (tt) cc_final: 0.6168 (tp) REVERT: A 1861 MET cc_start: 0.6636 (ttt) cc_final: 0.6403 (ttt) REVERT: A 1896 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8629 (mm) REVERT: A 1926 PHE cc_start: 0.7685 (t80) cc_final: 0.7422 (m-80) REVERT: A 1938 PHE cc_start: 0.7430 (t80) cc_final: 0.6675 (m-80) REVERT: A 2262 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6633 (t70) REVERT: A 2271 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7559 (m-40) REVERT: A 3068 MET cc_start: 0.8143 (ptm) cc_final: 0.7758 (ptp) REVERT: A 3161 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 3169 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7435 (mpp) REVERT: A 3217 GLU cc_start: -0.0339 (OUTLIER) cc_final: -0.2328 (tp30) REVERT: A 3501 SER cc_start: 0.8318 (t) cc_final: 0.8055 (p) REVERT: A 3731 LEU cc_start: 0.3458 (OUTLIER) cc_final: 0.2856 (pp) REVERT: A 4158 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8777 (mm) REVERT: A 4213 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8193 (ttm-80) REVERT: A 4454 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 4460 LEU cc_start: 0.8140 (tp) cc_final: 0.7789 (tp) REVERT: A 4516 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7421 (m) outliers start: 70 outliers final: 53 residues processed: 317 average time/residue: 0.4184 time to fit residues: 222.8786 Evaluate side-chains 324 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1738 TYR Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 2262 ASP Chi-restraints excluded: chain A residue 2271 ASN Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2366 GLU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4034 GLU Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4498 SER Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 261 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 204 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3032 GLN A3087 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4029 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099984 restraints weight = 44310.814| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.28 r_work: 0.3195 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22272 Z= 0.150 Angle : 0.560 16.203 30218 Z= 0.274 Chirality : 0.040 0.164 3402 Planarity : 0.004 0.045 3869 Dihedral : 6.108 80.404 3023 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.00 % Allowed : 22.79 % Favored : 74.21 % 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: 1.79 (0.16), residues: 2687 helix: 2.11 (0.13), residues: 1507 sheet: -0.51 (0.32), residues: 258 loop : 0.25 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.003 0.001 HIS A2857 PHE 0.016 0.001 PHE A1836 TYR 0.027 0.002 TYR A2792 ARG 0.006 0.000 ARG A4462 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1241) hydrogen bonds : angle 4.21864 ( 3633) covalent geometry : bond 0.00354 (22272) covalent geometry : angle 0.55969 (30218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 264 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1896 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8672 (mm) REVERT: A 1926 PHE cc_start: 0.7717 (t80) cc_final: 0.7415 (m-80) REVERT: A 1941 MET cc_start: 0.7700 (tmm) cc_final: 0.7442 (tmm) REVERT: A 1967 MET cc_start: 0.8522 (mmm) cc_final: 0.7822 (mmt) REVERT: A 2012 MET cc_start: 0.7688 (tpt) cc_final: 0.7382 (tpt) REVERT: A 2262 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6622 (t70) REVERT: A 2271 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7477 (m-40) REVERT: A 2537 TYR cc_start: 0.8044 (m-80) cc_final: 0.7683 (m-80) REVERT: A 2676 THR cc_start: 0.8969 (m) cc_final: 0.8390 (p) REVERT: A 2975 ASP cc_start: 0.8753 (t70) cc_final: 0.8286 (t0) REVERT: A 3006 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8210 (mm-30) REVERT: A 3068 MET cc_start: 0.8187 (ptm) cc_final: 0.7769 (ptp) REVERT: A 3169 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7477 (mpp) REVERT: A 3217 GLU cc_start: -0.0402 (OUTLIER) cc_final: -0.2325 (tp30) REVERT: A 3501 SER cc_start: 0.8302 (t) cc_final: 0.8028 (p) REVERT: A 3731 LEU cc_start: 0.3597 (OUTLIER) cc_final: 0.2967 (pp) REVERT: A 3938 LEU cc_start: 0.9442 (tt) cc_final: 0.9122 (tt) REVERT: A 4043 MET cc_start: 0.8262 (mmt) cc_final: 0.7653 (mmt) REVERT: A 4158 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8822 (mm) REVERT: A 4454 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7582 (mm-30) REVERT: A 4460 LEU cc_start: 0.8202 (tp) cc_final: 0.7917 (tp) REVERT: A 4516 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7430 (m) outliers start: 72 outliers final: 55 residues processed: 313 average time/residue: 0.2950 time to fit residues: 154.5733 Evaluate side-chains 317 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1685 MET Chi-restraints excluded: chain A residue 1738 TYR Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2262 ASP Chi-restraints excluded: chain A residue 2271 ASN Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2366 GLU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3113 MET Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3637 ASP Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3838 ASN Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4034 GLU Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4498 SER Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 155 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3087 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4029 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.130966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101819 restraints weight = 44262.854| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.39 r_work: 0.3218 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22272 Z= 0.115 Angle : 0.557 16.668 30218 Z= 0.272 Chirality : 0.039 0.161 3402 Planarity : 0.004 0.108 3869 Dihedral : 5.970 80.376 3023 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.67 % Allowed : 23.38 % Favored : 73.96 % 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: 1.82 (0.17), residues: 2687 helix: 2.13 (0.13), residues: 1507 sheet: -0.40 (0.33), residues: 247 loop : 0.23 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.009 0.001 HIS A3535 PHE 0.013 0.001 PHE A1836 TYR 0.027 0.001 TYR A2792 ARG 0.005 0.000 ARG A3937 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 1241) hydrogen bonds : angle 4.17536 ( 3633) covalent geometry : bond 0.00260 (22272) covalent geometry : angle 0.55705 (30218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5374 Ramachandran restraints generated. 2687 Oldfield, 0 Emsley, 2687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 263 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.6708 (ptp) cc_final: 0.6505 (mpp) REVERT: A 1857 LEU cc_start: 0.6468 (tt) cc_final: 0.6209 (tp) REVERT: A 1896 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8706 (mm) REVERT: A 1926 PHE cc_start: 0.7649 (t80) cc_final: 0.7397 (m-80) REVERT: A 1938 PHE cc_start: 0.7362 (t80) cc_final: 0.6513 (m-80) REVERT: A 1941 MET cc_start: 0.7680 (tmm) cc_final: 0.7450 (tmm) REVERT: A 2012 MET cc_start: 0.7713 (tpt) cc_final: 0.7407 (tpt) REVERT: A 2262 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6548 (t70) REVERT: A 2271 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7462 (m-40) REVERT: A 2676 THR cc_start: 0.9006 (m) cc_final: 0.8418 (p) REVERT: A 2975 ASP cc_start: 0.8742 (t70) cc_final: 0.8267 (t0) REVERT: A 3068 MET cc_start: 0.8133 (ptm) cc_final: 0.7732 (ptp) REVERT: A 3169 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7446 (mpp) REVERT: A 3217 GLU cc_start: -0.0284 (OUTLIER) cc_final: -0.2180 (tp30) REVERT: A 3501 SER cc_start: 0.8342 (t) cc_final: 0.8093 (p) REVERT: A 3731 LEU cc_start: 0.3664 (OUTLIER) cc_final: 0.3083 (pp) REVERT: A 3938 LEU cc_start: 0.9434 (tt) cc_final: 0.9135 (tt) REVERT: A 4043 MET cc_start: 0.8229 (mmt) cc_final: 0.7658 (mmt) REVERT: A 4158 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8792 (mm) REVERT: A 4377 MET cc_start: 0.7294 (mmm) cc_final: 0.6367 (mmm) REVERT: A 4454 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 4460 LEU cc_start: 0.8171 (tp) cc_final: 0.7878 (tp) REVERT: A 4516 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7441 (m) outliers start: 64 outliers final: 47 residues processed: 307 average time/residue: 0.3379 time to fit residues: 174.4013 Evaluate side-chains 309 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1738 TYR Chi-restraints excluded: chain A residue 1769 MET Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1928 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2262 ASP Chi-restraints excluded: chain A residue 2271 ASN Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2925 ILE Chi-restraints excluded: chain A residue 2934 LEU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3064 VAL Chi-restraints excluded: chain A residue 3069 ASN Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3146 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3507 CYS Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3947 LEU Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4034 GLU Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4158 LEU Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4380 LEU Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4498 SER Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 49 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3087 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4029 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.130619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101544 restraints weight = 44225.491| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.22 r_work: 0.3220 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22272 Z= 0.125 Angle : 0.559 15.604 30218 Z= 0.273 Chirality : 0.039 0.170 3402 Planarity : 0.004 0.091 3869 Dihedral : 5.890 80.768 3023 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.54 % Allowed : 23.50 % Favored : 73.96 % 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 (0.17), residues: 2687 helix: 2.12 (0.13), residues: 1505 sheet: -0.49 (0.32), residues: 257 loop : 0.26 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.007 0.001 HIS A3535 PHE 0.016 0.001 PHE A4260 TYR 0.035 0.001 TYR A4636 ARG 0.008 0.000 ARG A4263 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 1241) hydrogen bonds : angle 4.18318 ( 3633) covalent geometry : bond 0.00288 (22272) covalent geometry : angle 0.55876 (30218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11627.61 seconds wall clock time: 204 minutes 40.65 seconds (12280.65 seconds total)