Starting phenix.real_space_refine on Thu Jun 19 08:08:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmu_44711/06_2025/9bmu_44711.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmu_44711/06_2025/9bmu_44711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmu_44711/06_2025/9bmu_44711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmu_44711/06_2025/9bmu_44711.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmu_44711/06_2025/9bmu_44711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmu_44711/06_2025/9bmu_44711.cif" } resolution = 3.7 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 111 5.16 5 C 13839 2.51 5 N 3760 2.21 5 O 4057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21776 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2698, 21664 Classifications: {'peptide': 2698} Link IDs: {'PTRANS': 125, 'TRANS': 2572} Chain breaks: 6 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 12.31, per 1000 atoms: 0.57 Number of scatterers: 21776 At special positions: 0 Unit cell: (148.493, 164.992, 118.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 9 15.00 O 4057 8.00 N 3760 7.00 C 13839 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: 5.80 Conformation dependent library (CDL) restraints added in 2.8 seconds 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5128 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 17 sheets defined 60.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.664A pdb=" N PHE A1629 " --> pdb=" O PHE A1626 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 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 removed outlier: 3.544A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1770 through 1772 No H-bonds generated for 'chain 'A' and resid 1770 through 1772' Processing helix chain 'A' and resid 1777 through 1798 removed outlier: 3.912A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.819A 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 1924 Processing helix chain 'A' and resid 1938 through 1952 Processing helix chain 'A' and resid 1964 through 1986 Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 4.540A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (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: 3.707A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 3.523A 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 2152 through 2165 removed outlier: 4.183A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2190 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: 3.749A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2320 removed outlier: 3.528A pdb=" N LEU A2315 " --> pdb=" O TRP A2311 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A2319 " --> pdb=" O LEU A2315 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A2320 " --> pdb=" O ASN A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.589A 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 Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 4.036A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 4.044A pdb=" N ALA A2608 " --> pdb=" O THR A2604 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.981A 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 2731 removed outlier: 3.870A pdb=" N HIS A2730 " --> pdb=" O ARG A2726 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 3.528A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2757 through 2764 Proline residue: A2760 - end of helix removed outlier: 5.292A 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: 3.573A 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 Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.738A pdb=" N GLN A2928 " --> pdb=" O ARG A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.624A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3022 through 3041 Processing helix chain 'A' and resid 3046 through 3061 removed outlier: 3.596A pdb=" N LEU A3050 " --> pdb=" O SER A3046 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.815A pdb=" N HIS A3200 " --> pdb=" O GLU A3196 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3516 removed outlier: 3.657A pdb=" N PHE A3496 " --> pdb=" O THR A3492 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 4.017A 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: 4.145A 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 Processing helix chain 'A' and resid 3704 through 3720 Processing helix chain 'A' and resid 3721 through 3732 removed outlier: 3.507A pdb=" N ASP A3725 " --> pdb=" O ARG A3721 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A3732 " --> pdb=" O ARG A3728 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3755 Processing helix chain 'A' and resid 3763 through 3793 removed outlier: 3.960A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) Processing helix chain 'A' and resid 3793 through 3819 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.758A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) 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 3878 through 3895 removed outlier: 4.076A pdb=" N THR A3882 " --> pdb=" O GLN A3878 " (cutoff:3.500A) Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3940 Processing helix chain 'A' and resid 3941 through 3945 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 4.096A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (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 4015 through 4018 removed outlier: 4.315A pdb=" N MET A4018 " --> pdb=" O GLU A4015 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4015 through 4018' Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.632A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A4033 " --> pdb=" O HIS A4029 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.844A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.025A 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 4115 removed outlier: 3.706A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 removed outlier: 3.698A 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: 3.515A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4195 removed outlier: 3.872A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.623A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.603A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4325 through 4345 removed outlier: 4.382A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (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 4439 Processing helix chain 'A' and resid 4445 through 4457 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4500 through 4506 removed outlier: 4.038A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 4.175A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1842 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1902 through 1903 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 5.827A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (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 2221 removed outlier: 6.406A pdb=" N LEU A2220 " --> pdb=" O PHE A2343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2268 removed outlier: 3.763A pdb=" N THR A2276 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2617 through 2620 removed outlier: 6.095A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 4.089A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 5.734A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A2994 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A3067 " --> pdb=" O MET A2994 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3611 removed outlier: 6.259A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4069 removed outlier: 6.238A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4508 through 4510 removed outlier: 6.628A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 4.195A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3624 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: 12.90 Time building geometry restraints manager: 6.82 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: 7127 1.34 - 1.46: 2931 1.46 - 1.57: 11992 1.57 - 1.69: 12 1.69 - 1.81: 185 Bond restraints: 22247 Sorted by residual: bond pdb=" C VAL A4035 " pdb=" N LYS A4036 " ideal model delta sigma weight residual 1.331 1.282 0.049 2.07e-02 2.33e+03 5.56e+00 bond pdb=" CB MET A2603 " pdb=" CG MET A2603 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.25e+00 bond pdb=" CG MET A2603 " pdb=" SD MET A2603 " ideal model delta sigma weight residual 1.803 1.764 0.039 2.50e-02 1.60e+03 2.46e+00 bond pdb=" SD MET A4377 " pdb=" CE MET A4377 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.21e+00 bond pdb=" CA VAL A2070 " pdb=" CB VAL A2070 " ideal model delta sigma weight residual 1.539 1.531 0.008 5.40e-03 3.43e+04 2.17e+00 ... (remaining 22242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 29893 2.99 - 5.98: 265 5.98 - 8.97: 18 8.97 - 11.96: 3 11.96 - 14.94: 1 Bond angle restraints: 30180 Sorted by residual: angle pdb=" CB MET A2012 " pdb=" CG MET A2012 " pdb=" SD MET A2012 " ideal model delta sigma weight residual 112.70 97.76 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" CG MET A2603 " pdb=" SD MET A2603 " pdb=" CE MET A2603 " ideal model delta sigma weight residual 100.90 90.03 10.87 2.20e+00 2.07e-01 2.44e+01 angle pdb=" CA LYS A4629 " pdb=" CB LYS A4629 " pdb=" CG LYS A4629 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" N GLU A2782 " pdb=" CA GLU A2782 " pdb=" CB GLU A2782 " ideal model delta sigma weight residual 110.39 116.37 -5.98 1.66e+00 3.63e-01 1.30e+01 angle pdb=" C GLN A2781 " pdb=" N GLU A2782 " pdb=" CA GLU A2782 " ideal model delta sigma weight residual 120.72 115.04 5.68 1.67e+00 3.59e-01 1.16e+01 ... (remaining 30175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 13153 33.72 - 67.45: 282 67.45 - 101.17: 44 101.17 - 134.90: 1 134.90 - 168.62: 1 Dihedral angle restraints: 13481 sinusoidal: 5589 harmonic: 7892 Sorted by residual: dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual 300.00 131.38 168.62 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CA GLY A2229 " pdb=" C GLY A2229 " pdb=" N LYS A2230 " pdb=" CA LYS A2230 " ideal model delta harmonic sigma weight residual 180.00 -146.91 -33.09 0 5.00e+00 4.00e-02 4.38e+01 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 66.06 -126.06 1 2.00e+01 2.50e-03 3.81e+01 ... (remaining 13478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2367 0.042 - 0.083: 799 0.083 - 0.124: 210 0.124 - 0.166: 20 0.166 - 0.207: 2 Chirality restraints: 3398 Sorted by residual: chirality pdb=" CB ILE A4071 " pdb=" CA ILE A4071 " pdb=" CG1 ILE A4071 " pdb=" CG2 ILE A4071 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1' ADP A4703 " pdb=" C2' ADP A4703 " pdb=" N9 ADP A4703 " pdb=" O4' ADP A4703 " both_signs ideal model delta sigma weight residual False 2.48 2.67 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA GLU A2767 " pdb=" N GLU A2767 " pdb=" C GLU A2767 " pdb=" CB GLU A2767 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 3395 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A4222 " -0.021 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP A4222 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A4222 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A4222 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A4222 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A4222 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A4222 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4222 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4222 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A4222 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2584 " -0.028 2.00e-02 2.50e+03 1.84e-02 8.42e+00 pdb=" CG TRP A2584 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A2584 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A2584 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2584 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A2584 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A2584 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2584 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2584 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A2584 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A4534 " 0.018 2.00e-02 2.50e+03 1.66e-02 6.87e+00 pdb=" CG TRP A4534 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A4534 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A4534 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A4534 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A4534 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A4534 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4534 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4534 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A4534 " -0.001 2.00e-02 2.50e+03 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 270 2.59 - 3.17: 20475 3.17 - 3.75: 37052 3.75 - 4.32: 48284 4.32 - 4.90: 77436 Nonbonded interactions: 183517 Sorted by model distance: nonbonded pdb=" OD1 ASP A2995 " pdb=" OG1 THR A3067 " model vdw 2.018 3.040 nonbonded pdb=" OG SER A3046 " pdb=" OE1 GLU A3049 " model vdw 2.092 3.040 nonbonded pdb=" O GLY A3106 " pdb=" OG1 THR A3110 " model vdw 2.092 3.040 nonbonded pdb=" O GLU A3490 " pdb=" OG SER A3493 " model vdw 2.094 3.040 nonbonded pdb=" OH TYR A2086 " pdb=" OD2 ASP A2153 " model vdw 2.108 3.040 ... (remaining 183512 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 group one per residue 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 55.620 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 0.054 22247 Z= 0.202 Angle : 0.727 14.944 30180 Z= 0.381 Chirality : 0.043 0.207 3398 Planarity : 0.005 0.054 3864 Dihedral : 14.947 168.621 8353 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2684 helix: 1.08 (0.13), residues: 1496 sheet: -1.82 (0.32), residues: 222 loop : -0.09 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A4222 HIS 0.011 0.001 HIS A1810 PHE 0.041 0.002 PHE A2926 TYR 0.026 0.002 TYR A2901 ARG 0.013 0.001 ARG A1805 Details of bonding type rmsd hydrogen bonds : bond 0.13791 ( 1234) hydrogen bonds : angle 6.30099 ( 3624) covalent geometry : bond 0.00448 (22247) covalent geometry : angle 0.72724 (30180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2347 ASP cc_start: 0.6912 (t0) cc_final: 0.6600 (t0) REVERT: A 2603 MET cc_start: 0.8247 (ptt) cc_final: 0.7895 (ppp) REVERT: A 3043 MET cc_start: 0.7764 (mmp) cc_final: 0.7523 (mmm) REVERT: A 4043 MET cc_start: 0.7414 (mpp) cc_final: 0.6348 (mpp) REVERT: A 4223 LEU cc_start: 0.8730 (tp) cc_final: 0.8391 (mm) REVERT: A 4454 GLU cc_start: 0.8068 (tt0) cc_final: 0.7617 (tt0) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.3348 time to fit residues: 207.0685 Evaluate side-chains 271 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2849 ASN ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN A3650 ASN A3714 ASN A3852 HIS ** A3907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.101157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.079814 restraints weight = 78397.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.082122 restraints weight = 43737.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.083612 restraints weight = 29818.858| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 22247 Z= 0.288 Angle : 0.779 12.634 30180 Z= 0.396 Chirality : 0.047 0.201 3398 Planarity : 0.006 0.049 3864 Dihedral : 8.024 163.082 2997 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.84 % Allowed : 10.22 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2684 helix: 0.77 (0.13), residues: 1508 sheet: -1.85 (0.34), residues: 211 loop : -0.20 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A2584 HIS 0.011 0.001 HIS A1810 PHE 0.041 0.003 PHE A3094 TYR 0.019 0.003 TYR A2881 ARG 0.009 0.001 ARG A4462 Details of bonding type rmsd hydrogen bonds : bond 0.05018 ( 1234) hydrogen bonds : angle 5.42360 ( 3624) covalent geometry : bond 0.00648 (22247) covalent geometry : angle 0.77882 (30180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 309 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1631 PHE cc_start: 0.8124 (m-80) cc_final: 0.7865 (m-80) REVERT: A 1708 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6590 (tm-30) REVERT: A 1739 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7589 (mp) REVERT: A 1877 ASP cc_start: 0.7208 (t0) cc_final: 0.6796 (t0) REVERT: A 1897 GLU cc_start: 0.7858 (tt0) cc_final: 0.7550 (mt-10) REVERT: A 2063 GLU cc_start: 0.8226 (pp20) cc_final: 0.7876 (pt0) REVERT: A 2347 ASP cc_start: 0.7077 (t0) cc_final: 0.6513 (t0) REVERT: A 2507 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.7796 (mmm-85) REVERT: A 2510 MET cc_start: 0.8571 (mpp) cc_final: 0.8008 (mpp) REVERT: A 2603 MET cc_start: 0.8649 (ptt) cc_final: 0.8275 (ppp) REVERT: A 2615 MET cc_start: 0.7013 (mpp) cc_final: 0.6773 (mpp) REVERT: A 2668 LEU cc_start: 0.8695 (tp) cc_final: 0.8464 (tp) REVERT: A 2671 MET cc_start: 0.6693 (mmm) cc_final: 0.6476 (mmm) REVERT: A 2686 MET cc_start: 0.8803 (mmm) cc_final: 0.8441 (mmt) REVERT: A 2755 MET cc_start: 0.7439 (tpt) cc_final: 0.7202 (tpt) REVERT: A 2867 MET cc_start: 0.8324 (mpp) cc_final: 0.8113 (mpp) REVERT: A 3043 MET cc_start: 0.8113 (mmp) cc_final: 0.7821 (mmm) REVERT: A 3066 PHE cc_start: 0.7645 (t80) cc_final: 0.7162 (t80) REVERT: A 3154 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7028 (mm) REVERT: A 3811 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 4043 MET cc_start: 0.7834 (mpp) cc_final: 0.6428 (mpp) REVERT: A 4416 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8390 (mm-30) outliers start: 44 outliers final: 33 residues processed: 332 average time/residue: 0.3144 time to fit residues: 171.3438 Evaluate side-chains 295 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2127 ILE Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2532 ILE Chi-restraints excluded: chain A residue 2567 VAL Chi-restraints excluded: chain A residue 2614 ASP Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2774 VAL Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3811 ILE Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3890 ILE Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4056 GLU Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4210 SER Chi-restraints excluded: chain A residue 4219 VAL Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4395 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4514 LEU Chi-restraints excluded: chain A residue 4590 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 136 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.0970 chunk 235 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 222 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1841 GLN ** A2463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2725 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN A3197 GLN A3714 ASN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.105853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.084608 restraints weight = 74410.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.087067 restraints weight = 40604.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.088637 restraints weight = 27217.067| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22247 Z= 0.133 Angle : 0.642 10.502 30180 Z= 0.317 Chirality : 0.042 0.178 3398 Planarity : 0.004 0.055 3864 Dihedral : 7.445 160.882 2997 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.04 % Allowed : 12.77 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 2684 helix: 1.23 (0.13), residues: 1505 sheet: -1.85 (0.32), residues: 239 loop : 0.07 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A2584 HIS 0.007 0.001 HIS A2791 PHE 0.024 0.002 PHE A2682 TYR 0.022 0.002 TYR A3836 ARG 0.009 0.000 ARG A2046 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 1234) hydrogen bonds : angle 4.92720 ( 3624) covalent geometry : bond 0.00289 (22247) covalent geometry : angle 0.64248 (30180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 333 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8276 (mmm) cc_final: 0.8039 (mmm) REVERT: A 1708 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6426 (tm-30) REVERT: A 1738 TYR cc_start: 0.7560 (t80) cc_final: 0.7264 (t80) REVERT: A 1739 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7387 (mp) REVERT: A 2001 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5611 (mm) REVERT: A 2063 GLU cc_start: 0.8145 (pp20) cc_final: 0.7936 (pt0) REVERT: A 2347 ASP cc_start: 0.7256 (t0) cc_final: 0.6753 (t0) REVERT: A 2481 MET cc_start: 0.6896 (pmm) cc_final: 0.5860 (mmm) REVERT: A 2507 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.7863 (mmm-85) REVERT: A 2510 MET cc_start: 0.8562 (mpp) cc_final: 0.7820 (mpp) REVERT: A 2531 ASN cc_start: 0.8824 (t0) cc_final: 0.8598 (p0) REVERT: A 2603 MET cc_start: 0.8480 (ptt) cc_final: 0.8094 (ppp) REVERT: A 2668 LEU cc_start: 0.8643 (tp) cc_final: 0.8425 (tp) REVERT: A 2671 MET cc_start: 0.6642 (mmm) cc_final: 0.6371 (mmm) REVERT: A 2686 MET cc_start: 0.8792 (mmm) cc_final: 0.8423 (mmt) REVERT: A 2867 MET cc_start: 0.8239 (mpp) cc_final: 0.7973 (mpp) REVERT: A 2898 LYS cc_start: 0.9423 (mmtt) cc_final: 0.9133 (mmtt) REVERT: A 3043 MET cc_start: 0.8011 (mmp) cc_final: 0.7783 (mmm) REVERT: A 3066 PHE cc_start: 0.7641 (t80) cc_final: 0.7303 (t80) REVERT: A 3878 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 4043 MET cc_start: 0.7908 (mpp) cc_final: 0.6512 (mpp) REVERT: A 4129 GLU cc_start: 0.8264 (mp0) cc_final: 0.8029 (mp0) REVERT: A 4339 MET cc_start: 0.8321 (tpp) cc_final: 0.8081 (tpp) REVERT: A 4416 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8574 (mm-30) REVERT: A 4454 GLU cc_start: 0.7849 (tt0) cc_final: 0.7571 (tt0) REVERT: A 4570 CYS cc_start: 0.7655 (t) cc_final: 0.7424 (t) outliers start: 49 outliers final: 23 residues processed: 359 average time/residue: 0.3041 time to fit residues: 179.0073 Evaluate side-chains 308 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2782 GLU Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3197 GLN Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3890 ILE Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4590 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 2 optimal weight: 8.9990 chunk 238 optimal weight: 0.0870 chunk 266 optimal weight: 0.4980 chunk 239 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 153 optimal weight: 30.0000 chunk 169 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 242 optimal weight: 0.4980 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1856 GLN A2215 GLN A2217 ASN A2463 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 ASN A3522 GLN A3714 ASN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4566 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.104536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.082936 restraints weight = 77136.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.085433 restraints weight = 42386.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.087183 restraints weight = 28520.728| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22247 Z= 0.146 Angle : 0.645 12.458 30180 Z= 0.316 Chirality : 0.042 0.210 3398 Planarity : 0.004 0.046 3864 Dihedral : 7.254 161.189 2997 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.29 % Allowed : 14.31 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2684 helix: 1.29 (0.13), residues: 1514 sheet: -1.78 (0.32), residues: 228 loop : 0.01 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A2584 HIS 0.005 0.001 HIS A2791 PHE 0.022 0.002 PHE A3094 TYR 0.017 0.001 TYR A2967 ARG 0.006 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 1234) hydrogen bonds : angle 4.82707 ( 3624) covalent geometry : bond 0.00333 (22247) covalent geometry : angle 0.64531 (30180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8207 (mmm) cc_final: 0.7943 (mmm) REVERT: A 1702 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 1708 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 1739 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7368 (mp) REVERT: A 1856 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: A 1877 ASP cc_start: 0.7296 (t0) cc_final: 0.7034 (t0) REVERT: A 2001 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5462 (mm) REVERT: A 2106 GLU cc_start: 0.8053 (tt0) cc_final: 0.7550 (tm-30) REVERT: A 2347 ASP cc_start: 0.7157 (t0) cc_final: 0.6513 (t0) REVERT: A 2507 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.7987 (mmm-85) REVERT: A 2510 MET cc_start: 0.8516 (mpp) cc_final: 0.7982 (mpp) REVERT: A 2584 TRP cc_start: 0.8312 (m-10) cc_final: 0.8039 (m-10) REVERT: A 2603 MET cc_start: 0.8517 (ptt) cc_final: 0.8230 (ptp) REVERT: A 2668 LEU cc_start: 0.8670 (tp) cc_final: 0.8456 (tp) REVERT: A 2686 MET cc_start: 0.8757 (mmm) cc_final: 0.8392 (mmt) REVERT: A 2755 MET cc_start: 0.7242 (tpt) cc_final: 0.6944 (tpt) REVERT: A 2863 ARG cc_start: 0.7732 (tpt90) cc_final: 0.7491 (tpt90) REVERT: A 2867 MET cc_start: 0.8316 (mpp) cc_final: 0.7981 (mpp) REVERT: A 3043 MET cc_start: 0.8067 (mmp) cc_final: 0.7864 (mmm) REVERT: A 3494 GLU cc_start: 0.8300 (tt0) cc_final: 0.7867 (pm20) REVERT: A 3500 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8105 (mmp) REVERT: A 4013 LEU cc_start: 0.8575 (mt) cc_final: 0.8278 (mp) REVERT: A 4043 MET cc_start: 0.7891 (mpp) cc_final: 0.6554 (mpp) REVERT: A 4129 GLU cc_start: 0.8127 (mp0) cc_final: 0.7807 (mp0) REVERT: A 4416 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8584 (mm-30) REVERT: A 4454 GLU cc_start: 0.7953 (tt0) cc_final: 0.7738 (tt0) outliers start: 55 outliers final: 34 residues processed: 336 average time/residue: 0.3472 time to fit residues: 192.4362 Evaluate side-chains 315 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1856 GLN Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2532 ILE Chi-restraints excluded: chain A residue 2567 VAL Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2782 GLU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4219 VAL Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4395 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4481 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 56 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 258 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2463 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 ASN A3714 ASN ** A3865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS A4506 ASN ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.104403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.082819 restraints weight = 76929.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.085299 restraints weight = 42478.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.087017 restraints weight = 28649.796| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22247 Z= 0.150 Angle : 0.638 10.002 30180 Z= 0.313 Chirality : 0.042 0.249 3398 Planarity : 0.004 0.047 3864 Dihedral : 7.168 164.425 2997 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.96 % Allowed : 15.27 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2684 helix: 1.33 (0.13), residues: 1516 sheet: -1.78 (0.32), residues: 226 loop : 0.01 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A3093 HIS 0.005 0.001 HIS A3880 PHE 0.018 0.002 PHE A2727 TYR 0.019 0.001 TYR A3516 ARG 0.007 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 1234) hydrogen bonds : angle 4.76558 ( 3624) covalent geometry : bond 0.00341 (22247) covalent geometry : angle 0.63817 (30180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 300 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8154 (mmm) cc_final: 0.7897 (mmm) REVERT: A 1702 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7897 (mm) REVERT: A 1708 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 1739 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7410 (mp) REVERT: A 1889 TYR cc_start: 0.8891 (m-10) cc_final: 0.8173 (m-80) REVERT: A 2001 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5540 (mm) REVERT: A 2106 GLU cc_start: 0.8057 (tt0) cc_final: 0.7552 (tm-30) REVERT: A 2347 ASP cc_start: 0.7097 (t0) cc_final: 0.6395 (t0) REVERT: A 2507 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.7927 (mmm-85) REVERT: A 2510 MET cc_start: 0.8489 (mpp) cc_final: 0.7942 (mpp) REVERT: A 2668 LEU cc_start: 0.8664 (tp) cc_final: 0.8446 (tp) REVERT: A 2686 MET cc_start: 0.8786 (mmm) cc_final: 0.8454 (mmt) REVERT: A 3043 MET cc_start: 0.8082 (mmp) cc_final: 0.7878 (mmm) REVERT: A 3068 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5443 (ttt) REVERT: A 3500 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8146 (mmp) REVERT: A 3678 PHE cc_start: 0.8526 (m-80) cc_final: 0.8295 (m-80) REVERT: A 3811 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7342 (mp) REVERT: A 4013 LEU cc_start: 0.8698 (mt) cc_final: 0.8437 (mp) REVERT: A 4043 MET cc_start: 0.7882 (mpp) cc_final: 0.6557 (mpp) REVERT: A 4109 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5771 (mm) REVERT: A 4129 GLU cc_start: 0.8162 (mp0) cc_final: 0.7784 (mp0) REVERT: A 4339 MET cc_start: 0.8485 (tpp) cc_final: 0.8229 (tpp) REVERT: A 4416 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8596 (mm-30) REVERT: A 4454 GLU cc_start: 0.7956 (tt0) cc_final: 0.7613 (tt0) REVERT: A 4518 GLU cc_start: 0.8181 (pm20) cc_final: 0.7881 (tp30) REVERT: A 4570 CYS cc_start: 0.7944 (t) cc_final: 0.7583 (t) outliers start: 71 outliers final: 42 residues processed: 342 average time/residue: 0.2891 time to fit residues: 163.6578 Evaluate side-chains 328 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 2001 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2567 VAL Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2774 VAL Chi-restraints excluded: chain A residue 2782 GLU Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2830 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3811 ILE Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4109 LEU Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4219 VAL Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4310 GLU Chi-restraints excluded: chain A residue 4395 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4613 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 122 optimal weight: 0.0060 chunk 107 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 chunk 220 optimal weight: 7.9990 chunk 226 optimal weight: 0.7980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1818 GLN A1856 GLN A1922 GLN A2463 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3119 ASN A3714 ASN A4062 GLN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.106155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.084611 restraints weight = 76243.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087131 restraints weight = 41874.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.088960 restraints weight = 28182.145| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22247 Z= 0.124 Angle : 0.632 11.143 30180 Z= 0.308 Chirality : 0.041 0.263 3398 Planarity : 0.004 0.044 3864 Dihedral : 7.009 161.916 2997 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.71 % Allowed : 16.15 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 2684 helix: 1.44 (0.13), residues: 1513 sheet: -1.84 (0.32), residues: 235 loop : 0.09 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A2584 HIS 0.004 0.001 HIS A3880 PHE 0.030 0.001 PHE A2727 TYR 0.018 0.001 TYR A2967 ARG 0.005 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 1234) hydrogen bonds : angle 4.65923 ( 3624) covalent geometry : bond 0.00274 (22247) covalent geometry : angle 0.63216 (30180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 309 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8202 (mmm) cc_final: 0.7967 (mmm) REVERT: A 1702 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7872 (mm) REVERT: A 1708 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6650 (tm-30) REVERT: A 1739 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7427 (mp) REVERT: A 1889 TYR cc_start: 0.8858 (m-10) cc_final: 0.8182 (m-80) REVERT: A 1941 MET cc_start: 0.8370 (tpt) cc_final: 0.8154 (tpp) REVERT: A 2106 GLU cc_start: 0.8041 (tt0) cc_final: 0.7519 (tm-30) REVERT: A 2347 ASP cc_start: 0.7098 (t0) cc_final: 0.6397 (t0) REVERT: A 2481 MET cc_start: 0.7046 (pmm) cc_final: 0.5792 (tpp) REVERT: A 2507 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.8040 (mmm-85) REVERT: A 2510 MET cc_start: 0.8468 (mpp) cc_final: 0.7891 (mpp) REVERT: A 2594 CYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7632 (p) REVERT: A 2603 MET cc_start: 0.8517 (ptp) cc_final: 0.7960 (ppp) REVERT: A 2668 LEU cc_start: 0.8641 (tp) cc_final: 0.8429 (tp) REVERT: A 2686 MET cc_start: 0.8796 (mmm) cc_final: 0.8428 (mmt) REVERT: A 2898 LYS cc_start: 0.9389 (mmtt) cc_final: 0.9098 (mmtt) REVERT: A 3004 PHE cc_start: 0.4812 (m-80) cc_final: 0.4600 (m-10) REVERT: A 3043 MET cc_start: 0.8106 (mmp) cc_final: 0.7889 (mmm) REVERT: A 3068 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5342 (ttt) REVERT: A 3500 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8149 (mmp) REVERT: A 3590 ILE cc_start: 0.7203 (mt) cc_final: 0.6861 (tt) REVERT: A 3678 PHE cc_start: 0.8511 (m-80) cc_final: 0.8304 (m-80) REVERT: A 4013 LEU cc_start: 0.8722 (mt) cc_final: 0.8467 (mp) REVERT: A 4043 MET cc_start: 0.7896 (mpp) cc_final: 0.6560 (mpp) REVERT: A 4129 GLU cc_start: 0.8125 (mp0) cc_final: 0.7714 (mp0) REVERT: A 4158 LEU cc_start: 0.9191 (mt) cc_final: 0.8975 (mt) REVERT: A 4339 MET cc_start: 0.8455 (tpp) cc_final: 0.8251 (tpp) REVERT: A 4416 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8584 (mm-30) REVERT: A 4454 GLU cc_start: 0.8006 (tt0) cc_final: 0.7629 (tt0) outliers start: 65 outliers final: 39 residues processed: 352 average time/residue: 0.3977 time to fit residues: 234.1627 Evaluate side-chains 317 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 4.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2774 VAL Chi-restraints excluded: chain A residue 2782 GLU Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2830 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3713 LEU Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4210 SER Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4613 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 147 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3522 GLN A3714 ASN A3865 GLN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.103446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.082411 restraints weight = 76837.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.084829 restraints weight = 42121.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.086546 restraints weight = 28292.751| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22247 Z= 0.181 Angle : 0.688 11.543 30180 Z= 0.337 Chirality : 0.044 0.306 3398 Planarity : 0.004 0.045 3864 Dihedral : 7.077 165.731 2997 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.84 % Allowed : 17.31 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.16), residues: 2684 helix: 1.35 (0.13), residues: 1506 sheet: -1.91 (0.32), residues: 240 loop : 0.11 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A2584 HIS 0.004 0.001 HIS A1810 PHE 0.022 0.002 PHE A2692 TYR 0.022 0.002 TYR A3516 ARG 0.009 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 1234) hydrogen bonds : angle 4.79351 ( 3624) covalent geometry : bond 0.00413 (22247) covalent geometry : angle 0.68838 (30180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 282 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8220 (mmm) cc_final: 0.8001 (mmm) REVERT: A 1702 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7823 (mm) REVERT: A 1708 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6616 (tm-30) REVERT: A 1739 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7430 (mp) REVERT: A 1889 TYR cc_start: 0.8911 (m-10) cc_final: 0.8303 (m-80) REVERT: A 2041 MET cc_start: 0.8598 (mmt) cc_final: 0.8328 (mmt) REVERT: A 2106 GLU cc_start: 0.8047 (tt0) cc_final: 0.7526 (tm-30) REVERT: A 2348 LEU cc_start: 0.8591 (mt) cc_final: 0.7908 (pt) REVERT: A 2507 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8046 (mmm-85) REVERT: A 2510 MET cc_start: 0.8457 (mpp) cc_final: 0.7903 (mpp) REVERT: A 2603 MET cc_start: 0.8536 (ptp) cc_final: 0.8108 (ppp) REVERT: A 2668 LEU cc_start: 0.8630 (tp) cc_final: 0.8388 (tp) REVERT: A 2686 MET cc_start: 0.8842 (mmm) cc_final: 0.8469 (mmt) REVERT: A 2727 PHE cc_start: 0.7916 (t80) cc_final: 0.7464 (t80) REVERT: A 3004 PHE cc_start: 0.4939 (m-80) cc_final: 0.4644 (m-10) REVERT: A 3068 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5546 (ttt) REVERT: A 3500 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8094 (mmp) REVERT: A 3634 LEU cc_start: 0.9037 (pp) cc_final: 0.8809 (tp) REVERT: A 4013 LEU cc_start: 0.8782 (mt) cc_final: 0.8511 (mp) REVERT: A 4043 MET cc_start: 0.7635 (mpp) cc_final: 0.6167 (mpp) REVERT: A 4129 GLU cc_start: 0.8201 (mp0) cc_final: 0.7876 (mp0) REVERT: A 4416 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8596 (mm-30) REVERT: A 4454 GLU cc_start: 0.8095 (tt0) cc_final: 0.7787 (tt0) REVERT: A 4518 GLU cc_start: 0.8147 (pm20) cc_final: 0.7917 (tp30) REVERT: A 4570 CYS cc_start: 0.7854 (t) cc_final: 0.7535 (t) outliers start: 68 outliers final: 48 residues processed: 319 average time/residue: 0.3158 time to fit residues: 168.0989 Evaluate side-chains 313 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2774 VAL Chi-restraints excluded: chain A residue 2782 GLU Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2830 LEU Chi-restraints excluded: chain A residue 2838 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2926 PHE Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3713 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4002 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4219 VAL Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4395 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4613 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 6 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 33 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN A2463 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3714 ASN A3988 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.106153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.084753 restraints weight = 76562.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087307 restraints weight = 41836.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.089079 restraints weight = 27945.163| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22247 Z= 0.126 Angle : 0.669 14.710 30180 Z= 0.322 Chirality : 0.042 0.275 3398 Planarity : 0.004 0.047 3864 Dihedral : 6.948 162.772 2997 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.21 % Allowed : 18.11 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2684 helix: 1.43 (0.13), residues: 1513 sheet: -1.76 (0.31), residues: 245 loop : 0.08 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A2584 HIS 0.005 0.001 HIS A3880 PHE 0.022 0.001 PHE A2727 TYR 0.021 0.001 TYR A3641 ARG 0.007 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1234) hydrogen bonds : angle 4.66033 ( 3624) covalent geometry : bond 0.00281 (22247) covalent geometry : angle 0.66898 (30180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8198 (mmm) cc_final: 0.7996 (mmm) REVERT: A 1702 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7802 (mm) REVERT: A 1708 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6688 (tm-30) REVERT: A 1739 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7481 (mp) REVERT: A 1889 TYR cc_start: 0.8842 (m-10) cc_final: 0.8440 (m-80) REVERT: A 1941 MET cc_start: 0.8370 (tpp) cc_final: 0.7781 (tpp) REVERT: A 2041 MET cc_start: 0.8493 (mmt) cc_final: 0.8229 (mmt) REVERT: A 2106 GLU cc_start: 0.8022 (tt0) cc_final: 0.7504 (tm-30) REVERT: A 2348 LEU cc_start: 0.8250 (mt) cc_final: 0.7757 (pt) REVERT: A 2481 MET cc_start: 0.7036 (pmm) cc_final: 0.5877 (tpp) REVERT: A 2496 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.8017 (t80) REVERT: A 2507 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.7999 (mmm-85) REVERT: A 2510 MET cc_start: 0.8440 (mpp) cc_final: 0.7836 (mpp) REVERT: A 2603 MET cc_start: 0.8395 (ptp) cc_final: 0.7992 (ppp) REVERT: A 2668 LEU cc_start: 0.8640 (tp) cc_final: 0.8433 (tp) REVERT: A 2686 MET cc_start: 0.8828 (mmm) cc_final: 0.8461 (mmt) REVERT: A 2727 PHE cc_start: 0.7930 (t80) cc_final: 0.7628 (t80) REVERT: A 3004 PHE cc_start: 0.4763 (m-80) cc_final: 0.4511 (m-10) REVERT: A 3068 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5662 (ttt) REVERT: A 3500 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8071 (mmp) REVERT: A 3552 TYR cc_start: 0.8514 (t80) cc_final: 0.7833 (t80) REVERT: A 3590 ILE cc_start: 0.7183 (mt) cc_final: 0.6837 (tt) REVERT: A 4013 LEU cc_start: 0.8759 (mt) cc_final: 0.8501 (mp) REVERT: A 4043 MET cc_start: 0.7621 (mpp) cc_final: 0.6233 (mpp) REVERT: A 4105 TRP cc_start: 0.7065 (t60) cc_final: 0.6865 (t60) REVERT: A 4129 GLU cc_start: 0.8071 (mp0) cc_final: 0.7623 (mp0) REVERT: A 4339 MET cc_start: 0.8443 (tpp) cc_final: 0.8241 (tpp) REVERT: A 4416 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8588 (mm-30) REVERT: A 4454 GLU cc_start: 0.8109 (tt0) cc_final: 0.7884 (tt0) REVERT: A 4518 GLU cc_start: 0.8192 (pm20) cc_final: 0.7890 (tp30) outliers start: 53 outliers final: 39 residues processed: 326 average time/residue: 0.3194 time to fit residues: 173.7515 Evaluate side-chains 318 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2782 GLU Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2830 LEU Chi-restraints excluded: chain A residue 2838 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3713 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4210 SER Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4473 MET Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4605 VAL Chi-restraints excluded: chain A residue 4613 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 180 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN A2463 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3714 ASN A4062 GLN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.104063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.082915 restraints weight = 77120.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.085364 restraints weight = 42267.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.087053 restraints weight = 28442.137| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22247 Z= 0.167 Angle : 0.702 16.764 30180 Z= 0.338 Chirality : 0.044 0.304 3398 Planarity : 0.004 0.050 3864 Dihedral : 7.007 164.669 2997 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.59 % Allowed : 18.31 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2684 helix: 1.45 (0.13), residues: 1506 sheet: -1.87 (0.31), residues: 251 loop : 0.12 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A2584 HIS 0.006 0.001 HIS A4187 PHE 0.024 0.002 PHE A2036 TYR 0.019 0.002 TYR A3516 ARG 0.006 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 1234) hydrogen bonds : angle 4.71553 ( 3624) covalent geometry : bond 0.00382 (22247) covalent geometry : angle 0.70180 (30180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7826 (mm) REVERT: A 1708 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6747 (tm-30) REVERT: A 1739 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7509 (mp) REVERT: A 1889 TYR cc_start: 0.8851 (m-10) cc_final: 0.8496 (m-80) REVERT: A 1941 MET cc_start: 0.8521 (tpp) cc_final: 0.7536 (tpp) REVERT: A 2041 MET cc_start: 0.8660 (mmt) cc_final: 0.8358 (mmt) REVERT: A 2106 GLU cc_start: 0.8045 (tt0) cc_final: 0.7523 (tm-30) REVERT: A 2348 LEU cc_start: 0.8474 (mt) cc_final: 0.7870 (pt) REVERT: A 2349 LYS cc_start: 0.8874 (tmtt) cc_final: 0.8644 (tptp) REVERT: A 2496 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.8092 (t80) REVERT: A 2507 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8065 (mmm-85) REVERT: A 2510 MET cc_start: 0.8418 (mpp) cc_final: 0.7860 (mpp) REVERT: A 2668 LEU cc_start: 0.8583 (tp) cc_final: 0.8357 (tp) REVERT: A 3004 PHE cc_start: 0.4982 (m-80) cc_final: 0.4692 (m-10) REVERT: A 3068 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5902 (ttt) REVERT: A 3113 MET cc_start: 0.8540 (pmm) cc_final: 0.8312 (pmm) REVERT: A 3500 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8071 (mmp) REVERT: A 3552 TYR cc_start: 0.8630 (t80) cc_final: 0.7822 (t80) REVERT: A 4013 LEU cc_start: 0.8832 (mt) cc_final: 0.8545 (mp) REVERT: A 4043 MET cc_start: 0.7582 (mpp) cc_final: 0.6137 (mpp) REVERT: A 4129 GLU cc_start: 0.8197 (mp0) cc_final: 0.7662 (mp0) REVERT: A 4296 MET cc_start: 0.8608 (tpp) cc_final: 0.8188 (tpt) REVERT: A 4416 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8535 (mm-30) REVERT: A 4454 GLU cc_start: 0.8185 (tt0) cc_final: 0.7950 (tt0) outliers start: 62 outliers final: 51 residues processed: 305 average time/residue: 0.2945 time to fit residues: 150.2923 Evaluate side-chains 320 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1727 PHE Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1945 PHE Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2432 LEU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2594 CYS Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2701 VAL Chi-restraints excluded: chain A residue 2782 GLU Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2830 LEU Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3713 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4395 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4605 VAL Chi-restraints excluded: chain A residue 4613 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 158 optimal weight: 0.6980 chunk 266 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 93 optimal weight: 0.0070 chunk 203 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 200 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN A2463 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3714 ASN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.105070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083859 restraints weight = 76535.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.086396 restraints weight = 41418.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.088061 restraints weight = 27577.772| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22247 Z= 0.134 Angle : 0.712 18.505 30180 Z= 0.338 Chirality : 0.044 0.323 3398 Planarity : 0.004 0.051 3864 Dihedral : 6.973 165.170 2997 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.04 % Allowed : 18.94 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2684 helix: 1.46 (0.13), residues: 1506 sheet: -1.85 (0.31), residues: 251 loop : 0.16 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A2584 HIS 0.008 0.001 HIS A4187 PHE 0.024 0.002 PHE A2727 TYR 0.020 0.001 TYR A2967 ARG 0.006 0.000 ARG A3544 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 1234) hydrogen bonds : angle 4.66777 ( 3624) covalent geometry : bond 0.00306 (22247) covalent geometry : angle 0.71173 (30180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 275 time to evaluate : 5.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7811 (mm) REVERT: A 1708 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6715 (tm-30) REVERT: A 1739 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7495 (mp) REVERT: A 1889 TYR cc_start: 0.8829 (m-10) cc_final: 0.8489 (m-80) REVERT: A 1941 MET cc_start: 0.8490 (tpp) cc_final: 0.7571 (tpp) REVERT: A 2106 GLU cc_start: 0.8032 (tt0) cc_final: 0.7516 (tm-30) REVERT: A 2289 ASP cc_start: 0.8564 (m-30) cc_final: 0.8117 (p0) REVERT: A 2348 LEU cc_start: 0.8407 (mt) cc_final: 0.7876 (pt) REVERT: A 2349 LYS cc_start: 0.8862 (tmtt) cc_final: 0.8631 (tptp) REVERT: A 2481 MET cc_start: 0.7108 (pmm) cc_final: 0.5887 (tpp) REVERT: A 2496 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8030 (t80) REVERT: A 2507 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8049 (mmm-85) REVERT: A 2510 MET cc_start: 0.8418 (mpp) cc_final: 0.7841 (mpp) REVERT: A 2603 MET cc_start: 0.8361 (ptp) cc_final: 0.7992 (ppp) REVERT: A 2668 LEU cc_start: 0.8552 (tp) cc_final: 0.8324 (tp) REVERT: A 2727 PHE cc_start: 0.7472 (t80) cc_final: 0.7168 (t80) REVERT: A 3004 PHE cc_start: 0.4967 (m-80) cc_final: 0.4660 (m-10) REVERT: A 3068 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5523 (mtp) REVERT: A 3500 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8066 (mmp) REVERT: A 3552 TYR cc_start: 0.8535 (t80) cc_final: 0.8140 (t80) REVERT: A 3693 CYS cc_start: 0.5656 (OUTLIER) cc_final: 0.5204 (t) REVERT: A 4007 MET cc_start: 0.8599 (ptm) cc_final: 0.8233 (ppp) REVERT: A 4013 LEU cc_start: 0.8799 (mt) cc_final: 0.8524 (mp) REVERT: A 4043 MET cc_start: 0.7570 (mpp) cc_final: 0.6126 (mpp) REVERT: A 4129 GLU cc_start: 0.8120 (mp0) cc_final: 0.7610 (mp0) REVERT: A 4133 LYS cc_start: 0.9473 (mmmt) cc_final: 0.8876 (ttpp) REVERT: A 4296 MET cc_start: 0.8493 (tpp) cc_final: 0.8153 (tpt) REVERT: A 4416 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8631 (mm-30) REVERT: A 4454 GLU cc_start: 0.8153 (tt0) cc_final: 0.7912 (tt0) REVERT: A 4518 GLU cc_start: 0.8261 (pm20) cc_final: 0.7920 (tp30) REVERT: A 4613 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8470 (p90) outliers start: 49 outliers final: 39 residues processed: 305 average time/residue: 0.4380 time to fit residues: 226.8779 Evaluate side-chains 317 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 5.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1629 PHE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1894 GLN Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2432 LEU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2782 GLU Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2830 LEU Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3172 THR Chi-restraints excluded: chain A residue 3500 MET Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3679 LEU Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3693 CYS Chi-restraints excluded: chain A residue 3703 VAL Chi-restraints excluded: chain A residue 3713 LEU Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4106 LEU Chi-restraints excluded: chain A residue 4138 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4481 ASP Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4605 VAL Chi-restraints excluded: chain A residue 4613 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 221 optimal weight: 0.3980 chunk 149 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN A2463 HIS ** A2730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.103356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.081985 restraints weight = 77907.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.084389 restraints weight = 43167.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.086072 restraints weight = 29274.775| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22247 Z= 0.189 Angle : 0.725 16.184 30180 Z= 0.350 Chirality : 0.044 0.318 3398 Planarity : 0.004 0.050 3864 Dihedral : 6.969 168.315 2997 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.42 % Allowed : 18.56 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.16), residues: 2684 helix: 1.39 (0.13), residues: 1505 sheet: -1.88 (0.30), residues: 262 loop : 0.16 (0.22), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A2584 HIS 0.006 0.001 HIS A4187 PHE 0.024 0.002 PHE A2692 TYR 0.022 0.002 TYR A3516 ARG 0.005 0.000 ARG A4176 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 1234) hydrogen bonds : angle 4.75008 ( 3624) covalent geometry : bond 0.00434 (22247) covalent geometry : angle 0.72501 (30180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8531.29 seconds wall clock time: 152 minutes 48.89 seconds (9168.89 seconds total)