Starting phenix.real_space_refine on Sat May 24 00:45:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bma_44693/05_2025/9bma_44693.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bma_44693/05_2025/9bma_44693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bma_44693/05_2025/9bma_44693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bma_44693/05_2025/9bma_44693.map" model { file = "/net/cci-nas-00/data/ceres_data/9bma_44693/05_2025/9bma_44693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bma_44693/05_2025/9bma_44693.cif" } resolution = 3.2 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= -0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 122 5.16 5 C 15572 2.51 5 N 4223 2.21 5 O 4551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24476 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3029, 24390 Classifications: {'peptide': 3029} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2895} Chain breaks: 4 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' MG': 1, 'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 13.52, per 1000 atoms: 0.55 Number of scatterers: 24476 At special positions: 0 Unit cell: (128.7, 154.275, 177.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 122 16.00 P 7 15.00 Mg 1 11.99 O 4551 8.00 N 4223 7.00 C 15572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.40 Conformation dependent library (CDL) restraints added in 3.4 seconds 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 22 sheets defined 64.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 removed outlier: 4.081A pdb=" N LYS A1338 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A1339 " --> pdb=" O GLU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1372 Processing helix chain 'A' and resid 1374 through 1379 Processing helix chain 'A' and resid 1380 through 1396 removed outlier: 3.525A pdb=" N GLU A1384 " --> pdb=" O TYR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1405 removed outlier: 3.551A pdb=" N SER A1405 " --> pdb=" O ILE A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1421 Processing helix chain 'A' and resid 1425 through 1429 removed outlier: 3.623A pdb=" N LEU A1429 " --> pdb=" O VAL A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1437 Processing helix chain 'A' and resid 1442 through 1473 Processing helix chain 'A' and resid 1489 through 1508 Processing helix chain 'A' and resid 1516 through 1552 removed outlier: 3.744A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.272A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 removed outlier: 3.563A pdb=" N TYR A1630 " --> pdb=" O PRO A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1650 Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1697 through 1730 removed outlier: 4.117A pdb=" N THR A1703 " --> pdb=" O ASN A1699 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A1704 " --> pdb=" O GLU A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1775 through 1798 Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.587A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 1991 through 1995 removed outlier: 4.017A pdb=" N ALA A1995 " --> pdb=" O LYS A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 removed outlier: 3.671A pdb=" N VAL A2070 " --> pdb=" O ALA A2066 " (cutoff:3.500A) Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2131 Processing helix chain 'A' and resid 2132 through 2149 Proline residue: A2147 - end of helix Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.794A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A2297 " --> pdb=" O GLU A2294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2293 through 2297' Processing helix chain 'A' and resid 2312 through 2320 removed outlier: 4.446A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2359 Processing helix chain 'A' and resid 2365 through 2369 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2410 through 2424 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 removed outlier: 3.716A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2551 No H-bonds generated for 'chain 'A' and resid 2549 through 2551' Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.870A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.627A pdb=" N ALA A2579 " --> pdb=" O VAL A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.438A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 3.610A pdb=" N LEU A2744 " --> pdb=" O GLY A2740 " (cutoff:3.500A) Processing helix chain 'A' and resid 2757 through 2759 No H-bonds generated for 'chain 'A' and resid 2757 through 2759' Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.802A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.536A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2903 Processing helix chain 'A' and resid 2912 through 2927 removed outlier: 3.511A pdb=" N LEU A2920 " --> pdb=" O LEU A2916 " (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 2996 through 3000 Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.856A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.614A pdb=" N GLU A3035 " --> pdb=" O THR A3031 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3062 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.616A pdb=" N ASP A3077 " --> pdb=" O GLU A3073 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 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 3221 Processing helix chain 'A' and resid 3471 through 3501 Processing helix chain 'A' and resid 3502 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3580 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.747A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3608 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3734 Processing helix chain 'A' and resid 3736 through 3756 Processing helix chain 'A' and resid 3758 through 3763 removed outlier: 3.851A pdb=" N ASP A3762 " --> pdb=" O GLY A3758 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A3763 " --> pdb=" O ARG A3759 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3758 through 3763' Processing helix chain 'A' and resid 3765 through 3786 removed outlier: 4.101A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3818 removed outlier: 3.647A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3872 removed outlier: 3.689A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) 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 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.076A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.637A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.038A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4015 through 4017 No H-bonds generated for 'chain 'A' and resid 4015 through 4017' Processing helix chain 'A' and resid 4018 through 4023 Processing helix chain 'A' and resid 4026 through 4033 Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.689A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 3.926A pdb=" N ASN A4078 " --> pdb=" O ALA A4074 " (cutoff:3.500A) removed outlier: 4.144A 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: 3.575A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4141 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.300A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.714A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4287 through 4291 removed outlier: 3.763A pdb=" N GLY A4290 " --> pdb=" O LYS A4287 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 removed outlier: 4.231A pdb=" N LEU A4321 " --> pdb=" O THR A4317 " (cutoff:3.500A) Processing helix chain 'A' and resid 4325 through 4353 removed outlier: 4.138A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A4353 " --> pdb=" O LEU A4349 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.365A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4499 Processing helix chain 'A' and resid 4501 through 4506 Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4639 Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.263A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.360A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2219 through 2221 Processing sheet with id=AA8, first strand: chain 'A' and resid 2267 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2592 through 2594 Processing sheet with id=AB3, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 3.641A pdb=" N VAL A2709 " --> pdb=" O LEU A2661 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 3.516A pdb=" N ALA A2651 " --> pdb=" O GLU A2640 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.695A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.765A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.530A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB9, first strand: chain 'A' and resid 4041 through 4045 removed outlier: 6.463A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.566A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.377A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 4539 through 4543 Processing sheet with id=AC4, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.770A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A4563 " --> pdb=" O LEU A4585 " (cutoff:3.500A) 1458 hydrogen bonds defined for protein. 4260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.10 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6524 1.33 - 1.45: 4471 1.45 - 1.58: 13787 1.58 - 1.70: 11 1.70 - 1.82: 206 Bond restraints: 24999 Sorted by residual: bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP A4702 " pdb=" C5 ADP A4702 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 ADP A4703 " pdb=" C6 ADP A4703 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C5 ADP A4702 " pdb=" C6 ADP A4702 " ideal model delta sigma weight residual 1.490 1.409 0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" CA PRO A2596 " pdb=" C PRO A2596 " ideal model delta sigma weight residual 1.514 1.534 -0.020 5.50e-03 3.31e+04 1.27e+01 ... (remaining 24994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 33421 2.34 - 4.69: 402 4.69 - 7.03: 44 7.03 - 9.37: 20 9.37 - 11.71: 8 Bond angle restraints: 33895 Sorted by residual: angle pdb=" PB ATP A4701 " pdb=" O3B ATP A4701 " pdb=" PG ATP A4701 " ideal model delta sigma weight residual 139.87 131.47 8.40 1.00e+00 1.00e+00 7.06e+01 angle pdb=" PA ATP A4701 " pdb=" O3A ATP A4701 " pdb=" PB ATP A4701 " ideal model delta sigma weight residual 136.83 128.87 7.96 1.00e+00 1.00e+00 6.34e+01 angle pdb=" C THR A4628 " pdb=" CA THR A4628 " pdb=" CB THR A4628 " ideal model delta sigma weight residual 116.54 110.94 5.60 1.15e+00 7.56e-01 2.37e+01 angle pdb=" PA ADP A4702 " pdb=" O3A ADP A4702 " pdb=" PB ADP A4702 " ideal model delta sigma weight residual 120.50 132.21 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB MET A3008 " pdb=" CG MET A3008 " pdb=" SD MET A3008 " ideal model delta sigma weight residual 112.70 124.31 -11.61 3.00e+00 1.11e-01 1.50e+01 ... (remaining 33890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.42: 14032 25.42 - 50.85: 971 50.85 - 76.27: 148 76.27 - 101.70: 20 101.70 - 127.12: 1 Dihedral angle restraints: 15172 sinusoidal: 6299 harmonic: 8873 Sorted by residual: dihedral pdb=" C5' ADP A4702 " pdb=" O5' ADP A4702 " pdb=" PA ADP A4702 " pdb=" O2A ADP A4702 " ideal model delta sinusoidal sigma weight residual -60.00 67.12 -127.12 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" CA THR A4127 " pdb=" C THR A4127 " pdb=" N MET A4128 " pdb=" CA MET A4128 " ideal model delta harmonic sigma weight residual -180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CG ARG A3782 " pdb=" CD ARG A3782 " pdb=" NE ARG A3782 " pdb=" CZ ARG A3782 " ideal model delta sinusoidal sigma weight residual 90.00 41.28 48.72 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 15169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2964 0.045 - 0.089: 637 0.089 - 0.134: 181 0.134 - 0.179: 20 0.179 - 0.223: 4 Chirality restraints: 3806 Sorted by residual: chirality pdb=" CB ILE A2871 " pdb=" CA ILE A2871 " pdb=" CG1 ILE A2871 " pdb=" CG2 ILE A2871 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE A1611 " pdb=" N ILE A1611 " pdb=" C ILE A1611 " pdb=" CB ILE A1611 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA ILE A4626 " pdb=" N ILE A4626 " pdb=" C ILE A4626 " pdb=" CB ILE A4626 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 3803 not shown) Planarity restraints: 4343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1435 " -0.025 2.00e-02 2.50e+03 2.64e-02 1.74e+01 pdb=" CG TRP A1435 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A1435 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A1435 " 0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP A1435 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A1435 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1435 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1435 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1435 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A1435 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A4117 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A4118 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A4118 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A4118 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1355 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO A1356 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A1356 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1356 " 0.038 5.00e-02 4.00e+02 ... (remaining 4340 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 80 2.45 - 3.06: 16765 3.06 - 3.68: 37957 3.68 - 4.29: 55863 4.29 - 4.90: 94358 Nonbonded interactions: 205023 Sorted by model distance: nonbonded pdb=" O1B ATP A4701 " pdb="MG MG A4704 " model vdw 1.841 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4704 " model vdw 1.908 2.170 nonbonded pdb=" OH TYR A4180 " pdb=" OD2 ASP A4220 " model vdw 2.162 3.040 nonbonded pdb=" O ILE A3766 " pdb=" OG1 THR A3769 " model vdw 2.193 3.040 nonbonded pdb=" OG SER A1691 " pdb=" OE1 GLU A1694 " model vdw 2.199 3.040 ... (remaining 205018 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 58.960 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 24999 Z= 0.226 Angle : 0.647 11.713 33895 Z= 0.353 Chirality : 0.041 0.223 3806 Planarity : 0.005 0.104 4343 Dihedral : 16.525 127.120 9406 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 0.15 % Allowed : 17.58 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.16), residues: 3019 helix: 2.04 (0.12), residues: 1785 sheet: -1.41 (0.35), residues: 214 loop : 0.13 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP A1435 HIS 0.007 0.001 HIS A4389 PHE 0.033 0.001 PHE A2949 TYR 0.019 0.001 TYR A1393 ARG 0.011 0.000 ARG A3782 Details of bonding type rmsd hydrogen bonds : bond 0.10700 ( 1458) hydrogen bonds : angle 5.09683 ( 4260) covalent geometry : bond 0.00427 (24999) covalent geometry : angle 0.64728 (33895) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 336 time to evaluate : 2.947 Fit side-chains revert: symmetry clash REVERT: A 2510 MET cc_start: 0.7680 (mmm) cc_final: 0.7332 (mmt) REVERT: A 2610 ARG cc_start: 0.7846 (ttm110) cc_final: 0.7176 (mtm110) REVERT: A 3741 ARG cc_start: 0.7572 (ttm170) cc_final: 0.7348 (ttm170) REVERT: A 3830 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7567 (tp-100) REVERT: A 4594 LYS cc_start: 0.7783 (tppt) cc_final: 0.7562 (tttp) outliers start: 4 outliers final: 2 residues processed: 340 average time/residue: 0.4185 time to fit residues: 216.1596 Evaluate side-chains 258 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 256 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2626 THR Chi-restraints excluded: chain A residue 2998 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 176 optimal weight: 0.0980 chunk 274 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1961 ASN ** A2130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2827 HIS A2875 ASN A3047 HIS A3087 ASN A3735 GLN A4012 ASN A4023 GLN A4029 HIS A4231 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112925 restraints weight = 32725.689| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.47 r_work: 0.3204 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24999 Z= 0.139 Angle : 0.532 7.779 33895 Z= 0.265 Chirality : 0.039 0.154 3806 Planarity : 0.004 0.074 4343 Dihedral : 5.661 130.896 3351 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.15 % Allowed : 16.84 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.16), residues: 3019 helix: 2.11 (0.12), residues: 1800 sheet: -1.38 (0.35), residues: 203 loop : 0.17 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1435 HIS 0.004 0.001 HIS A1412 PHE 0.015 0.001 PHE A3813 TYR 0.036 0.001 TYR A1393 ARG 0.005 0.000 ARG A3007 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 1458) hydrogen bonds : angle 4.32258 ( 4260) covalent geometry : bond 0.00322 (24999) covalent geometry : angle 0.53168 (33895) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 290 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1393 TYR cc_start: 0.6752 (m-80) cc_final: 0.6376 (m-80) REVERT: A 1448 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8137 (t0) REVERT: A 2169 GLN cc_start: 0.7622 (pm20) cc_final: 0.6639 (mm-40) REVERT: A 2475 ASN cc_start: 0.7994 (t0) cc_final: 0.7782 (m-40) REVERT: A 2505 ASP cc_start: 0.8940 (p0) cc_final: 0.8713 (p0) REVERT: A 2610 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7299 (mtm110) REVERT: A 3117 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7598 (ttpt) REVERT: A 3167 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7517 (mtm-85) REVERT: A 3499 GLN cc_start: 0.8268 (mt0) cc_final: 0.7877 (tp40) REVERT: A 3741 ARG cc_start: 0.7652 (ttm170) cc_final: 0.7339 (ttm170) REVERT: A 3830 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7924 (tp-100) REVERT: A 3834 ASP cc_start: 0.8035 (m-30) cc_final: 0.7550 (m-30) REVERT: A 4004 MET cc_start: 0.8481 (tpt) cc_final: 0.7988 (tpt) outliers start: 58 outliers final: 22 residues processed: 330 average time/residue: 0.3898 time to fit residues: 204.4233 Evaluate side-chains 282 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1435 TRP Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1961 ASN Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2521 ILE Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 3117 LYS Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 3972 TYR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4293 ASP Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4448 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 106 optimal weight: 0.8980 chunk 208 optimal weight: 0.8980 chunk 281 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 63 optimal weight: 0.0010 chunk 76 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1961 ASN A3047 HIS A4012 ASN A4174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.147180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111626 restraints weight = 32653.786| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.49 r_work: 0.3206 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24999 Z= 0.133 Angle : 0.509 9.087 33895 Z= 0.254 Chirality : 0.039 0.150 3806 Planarity : 0.004 0.051 4343 Dihedral : 5.452 116.062 3348 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.08 % Allowed : 17.21 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.16), residues: 3019 helix: 2.16 (0.12), residues: 1800 sheet: -1.52 (0.34), residues: 211 loop : 0.18 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1435 HIS 0.005 0.001 HIS A4389 PHE 0.015 0.001 PHE A3813 TYR 0.024 0.001 TYR A1393 ARG 0.004 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1458) hydrogen bonds : angle 4.18333 ( 4260) covalent geometry : bond 0.00307 (24999) covalent geometry : angle 0.50851 (33895) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 284 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1393 TYR cc_start: 0.6717 (m-10) cc_final: 0.6419 (m-80) REVERT: A 1448 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8133 (t0) REVERT: A 2129 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7785 (tp30) REVERT: A 2180 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7117 (mp0) REVERT: A 2310 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7680 (mp0) REVERT: A 2438 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7366 (mt-10) REVERT: A 2475 ASN cc_start: 0.7993 (t0) cc_final: 0.7770 (m-40) REVERT: A 2610 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7293 (mtm110) REVERT: A 2615 MET cc_start: 0.8870 (mmt) cc_final: 0.8563 (mmt) REVERT: A 3117 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7585 (ttpt) REVERT: A 3167 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7496 (mtm-85) REVERT: A 3499 GLN cc_start: 0.8284 (mt0) cc_final: 0.7924 (tp40) REVERT: A 3668 ASP cc_start: 0.7157 (p0) cc_final: 0.6750 (p0) REVERT: A 3830 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7915 (tp-100) REVERT: A 3834 ASP cc_start: 0.8049 (m-30) cc_final: 0.7556 (m-30) REVERT: A 4004 MET cc_start: 0.8481 (tpt) cc_final: 0.8042 (tpt) REVERT: A 4092 ARG cc_start: 0.6600 (mmp-170) cc_final: 0.6218 (ptt180) outliers start: 56 outliers final: 31 residues processed: 321 average time/residue: 0.3629 time to fit residues: 186.8113 Evaluate side-chains 284 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1435 TRP Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2281 THR Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2521 ILE Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2626 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3117 LYS Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4293 ASP Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 222 optimal weight: 0.2980 chunk 133 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.148851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113626 restraints weight = 32886.543| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.48 r_work: 0.3215 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24999 Z= 0.115 Angle : 0.489 7.956 33895 Z= 0.243 Chirality : 0.038 0.143 3806 Planarity : 0.004 0.043 4343 Dihedral : 5.240 106.099 3348 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.63 % Allowed : 17.62 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.16), residues: 3019 helix: 2.25 (0.12), residues: 1801 sheet: -1.52 (0.33), residues: 214 loop : 0.25 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A4478 HIS 0.007 0.001 HIS A4389 PHE 0.014 0.001 PHE A3813 TYR 0.021 0.001 TYR A1393 ARG 0.006 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 1458) hydrogen bonds : angle 4.04588 ( 4260) covalent geometry : bond 0.00261 (24999) covalent geometry : angle 0.48882 (33895) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1393 TYR cc_start: 0.6780 (m-10) cc_final: 0.6370 (m-80) REVERT: A 1435 TRP cc_start: 0.8067 (OUTLIER) cc_final: 0.7742 (m-10) REVERT: A 1448 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8124 (t0) REVERT: A 2129 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7691 (tp30) REVERT: A 2180 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7145 (mp0) REVERT: A 2217 ASN cc_start: 0.6749 (m110) cc_final: 0.6499 (m-40) REVERT: A 2310 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7593 (mp0) REVERT: A 2475 ASN cc_start: 0.8045 (t0) cc_final: 0.7795 (m-40) REVERT: A 2610 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7269 (mtm110) REVERT: A 2615 MET cc_start: 0.8821 (mmt) cc_final: 0.8527 (mmt) REVERT: A 2863 ARG cc_start: 0.7601 (tmt170) cc_final: 0.7282 (tpt90) REVERT: A 3117 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7654 (tttt) REVERT: A 3167 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7467 (mtm-85) REVERT: A 3202 ASN cc_start: 0.7399 (t0) cc_final: 0.7016 (m-40) REVERT: A 3499 GLN cc_start: 0.8311 (mt0) cc_final: 0.7970 (tp40) REVERT: A 3537 GLN cc_start: 0.8305 (tt0) cc_final: 0.8044 (tp40) REVERT: A 3668 ASP cc_start: 0.7090 (p0) cc_final: 0.6684 (p0) REVERT: A 3683 ASP cc_start: 0.8724 (t0) cc_final: 0.8497 (t0) REVERT: A 3737 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: A 3830 GLN cc_start: 0.8324 (tp-100) cc_final: 0.7914 (tp-100) REVERT: A 3834 ASP cc_start: 0.8042 (m-30) cc_final: 0.7539 (m-30) REVERT: A 4346 MET cc_start: 0.8128 (mmp) cc_final: 0.7712 (mmm) outliers start: 71 outliers final: 38 residues processed: 328 average time/residue: 0.3531 time to fit residues: 185.4393 Evaluate side-chains 297 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1435 TRP Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2521 ILE Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2626 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3117 LYS Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3572 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3661 LEU Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3737 GLU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4293 ASP Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 276 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 202 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2005 GLN A2377 ASN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.146585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111362 restraints weight = 33003.305| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.58 r_work: 0.3185 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24999 Z= 0.154 Angle : 0.512 8.032 33895 Z= 0.254 Chirality : 0.039 0.145 3806 Planarity : 0.004 0.041 4343 Dihedral : 5.203 101.621 3348 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.45 % Allowed : 17.92 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.16), residues: 3019 helix: 2.16 (0.12), residues: 1807 sheet: -1.50 (0.33), residues: 214 loop : 0.16 (0.21), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A4478 HIS 0.005 0.001 HIS A1500 PHE 0.016 0.001 PHE A3813 TYR 0.017 0.001 TYR A1393 ARG 0.004 0.000 ARG A4400 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1458) hydrogen bonds : angle 4.08798 ( 4260) covalent geometry : bond 0.00369 (24999) covalent geometry : angle 0.51217 (33895) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 277 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1448 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8151 (t0) REVERT: A 2129 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7722 (tp30) REVERT: A 2169 GLN cc_start: 0.7654 (pm20) cc_final: 0.6690 (mm-40) REVERT: A 2475 ASN cc_start: 0.7999 (t0) cc_final: 0.7747 (m-40) REVERT: A 2610 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7322 (mtm110) REVERT: A 2615 MET cc_start: 0.8906 (mmt) cc_final: 0.8498 (mmt) REVERT: A 2671 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7665 (mtt) REVERT: A 2813 LEU cc_start: 0.8098 (mt) cc_final: 0.7882 (mp) REVERT: A 3117 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7597 (tttt) REVERT: A 3167 ARG cc_start: 0.7745 (mtm-85) cc_final: 0.7486 (mtm-85) REVERT: A 3499 GLN cc_start: 0.8377 (mt0) cc_final: 0.8052 (tp40) REVERT: A 3537 GLN cc_start: 0.8331 (tt0) cc_final: 0.8055 (tp40) REVERT: A 3668 ASP cc_start: 0.7198 (p0) cc_final: 0.6786 (p0) REVERT: A 3683 ASP cc_start: 0.8811 (t0) cc_final: 0.8553 (t0) REVERT: A 3737 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: A 3830 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7958 (tp-100) REVERT: A 3834 ASP cc_start: 0.8038 (m-30) cc_final: 0.7543 (m-30) outliers start: 66 outliers final: 45 residues processed: 322 average time/residue: 0.3709 time to fit residues: 191.4757 Evaluate side-chains 302 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2281 THR Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2521 ILE Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2626 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3117 LYS Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3737 GLU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4293 ASP Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 233 optimal weight: 6.9990 chunk 290 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1961 ASN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112370 restraints weight = 32762.722| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.47 r_work: 0.3196 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.003 0.032 24999 Z= 0.127 Angle : 0.502 8.691 33895 Z= 0.248 Chirality : 0.038 0.144 3806 Planarity : 0.004 0.041 4343 Dihedral : 5.100 97.025 3348 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.56 % Allowed : 18.03 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 3019 helix: 2.21 (0.12), residues: 1807 sheet: -1.47 (0.33), residues: 214 loop : 0.18 (0.21), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1435 HIS 0.005 0.001 HIS A4389 PHE 0.015 0.001 PHE A3813 TYR 0.018 0.001 TYR A1393 ARG 0.006 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 1458) hydrogen bonds : angle 4.03634 ( 4260) covalent geometry : bond 0.00297 (24999) covalent geometry : angle 0.50159 (33895) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 285 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1448 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8134 (t0) REVERT: A 2129 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7728 (tp30) REVERT: A 2169 GLN cc_start: 0.7667 (pm20) cc_final: 0.6722 (mm-40) REVERT: A 2180 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7094 (mp0) REVERT: A 2310 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7595 (mp0) REVERT: A 2438 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7515 (mt-10) REVERT: A 2610 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7319 (mtm110) REVERT: A 2615 MET cc_start: 0.8875 (mmt) cc_final: 0.8456 (mmt) REVERT: A 2793 ILE cc_start: 0.8697 (pt) cc_final: 0.8463 (mt) REVERT: A 2863 ARG cc_start: 0.7608 (tmt170) cc_final: 0.7283 (tpt90) REVERT: A 2879 LYS cc_start: 0.8398 (tppt) cc_final: 0.7568 (ttpp) REVERT: A 3117 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7644 (tttt) REVERT: A 3167 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7512 (mtm-85) REVERT: A 3202 ASN cc_start: 0.7394 (t0) cc_final: 0.7017 (m-40) REVERT: A 3499 GLN cc_start: 0.8379 (mt0) cc_final: 0.8042 (tp40) REVERT: A 3537 GLN cc_start: 0.8315 (tt0) cc_final: 0.8048 (tp40) REVERT: A 3668 ASP cc_start: 0.7129 (p0) cc_final: 0.6740 (p0) REVERT: A 3683 ASP cc_start: 0.8803 (t0) cc_final: 0.8538 (t0) REVERT: A 3737 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: A 3834 ASP cc_start: 0.8067 (m-30) cc_final: 0.7717 (m-30) REVERT: A 4021 MET cc_start: 0.8383 (mmp) cc_final: 0.8104 (mmm) outliers start: 69 outliers final: 50 residues processed: 338 average time/residue: 0.3534 time to fit residues: 191.5304 Evaluate side-chains 313 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 1961 ASN Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2521 ILE Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2626 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2761 SER Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3117 LYS Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3661 LEU Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3737 GLU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 4012 ASN Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4293 ASP Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 287 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 256 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1667 ASN A1790 ASN A3200 HIS A3744 GLN ** A3754 ASN ** 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 = 0.3829 r_free = 0.3829 target = 0.147898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112847 restraints weight = 32894.649| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.54 r_work: 0.3206 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24999 Z= 0.120 Angle : 0.497 8.355 33895 Z= 0.246 Chirality : 0.038 0.144 3806 Planarity : 0.004 0.041 4343 Dihedral : 5.025 93.899 3348 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.52 % Allowed : 18.14 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.16), residues: 3019 helix: 2.26 (0.12), residues: 1806 sheet: -1.44 (0.34), residues: 214 loop : 0.20 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1435 HIS 0.005 0.001 HIS A4389 PHE 0.020 0.001 PHE A4410 TYR 0.023 0.001 TYR A1393 ARG 0.004 0.000 ARG A1962 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 1458) hydrogen bonds : angle 4.00565 ( 4260) covalent geometry : bond 0.00278 (24999) covalent geometry : angle 0.49705 (33895) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1448 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8125 (t0) REVERT: A 1667 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7861 (m110) REVERT: A 1847 ASP cc_start: 0.8298 (t0) cc_final: 0.7997 (t0) REVERT: A 2129 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7731 (tp30) REVERT: A 2169 GLN cc_start: 0.7654 (pm20) cc_final: 0.6707 (mm-40) REVERT: A 2180 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7081 (mp0) REVERT: A 2438 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7547 (mt-10) REVERT: A 2610 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7295 (mtm110) REVERT: A 2615 MET cc_start: 0.8876 (mmt) cc_final: 0.8408 (mmt) REVERT: A 2671 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7663 (mtt) REVERT: A 2793 ILE cc_start: 0.8677 (pt) cc_final: 0.8451 (mt) REVERT: A 2863 ARG cc_start: 0.7621 (tmt170) cc_final: 0.7292 (tpt90) REVERT: A 2879 LYS cc_start: 0.8410 (tppt) cc_final: 0.7555 (ttpp) REVERT: A 3117 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7629 (tttt) REVERT: A 3167 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7499 (mtm-85) REVERT: A 3202 ASN cc_start: 0.7414 (t0) cc_final: 0.7028 (m-40) REVERT: A 3486 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5405 (ttp80) REVERT: A 3499 GLN cc_start: 0.8365 (mt0) cc_final: 0.8030 (tp40) REVERT: A 3537 GLN cc_start: 0.8310 (tt0) cc_final: 0.8030 (tp40) REVERT: A 3668 ASP cc_start: 0.7124 (p0) cc_final: 0.6724 (p0) REVERT: A 3683 ASP cc_start: 0.8795 (t0) cc_final: 0.8536 (t0) REVERT: A 3737 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7198 (tt0) outliers start: 68 outliers final: 54 residues processed: 327 average time/residue: 0.3705 time to fit residues: 194.8822 Evaluate side-chains 324 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1667 ASN Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2281 THR Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2521 ILE Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2626 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2761 SER Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3117 LYS Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3135 GLN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3486 ARG Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3661 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3737 GLU Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 4012 ASN Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4293 ASP Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 144 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 chunk 234 optimal weight: 0.0870 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 299 optimal weight: 0.3980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111663 restraints weight = 33155.222| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.77 r_work: 0.3187 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24999 Z= 0.120 Angle : 0.502 9.524 33895 Z= 0.248 Chirality : 0.038 0.144 3806 Planarity : 0.004 0.041 4343 Dihedral : 4.968 91.424 3348 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.52 % Allowed : 18.25 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.16), residues: 3019 helix: 2.28 (0.12), residues: 1806 sheet: -1.42 (0.34), residues: 214 loop : 0.19 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1435 HIS 0.005 0.001 HIS A4389 PHE 0.015 0.001 PHE A3813 TYR 0.016 0.001 TYR A2748 ARG 0.004 0.000 ARG A1488 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1458) hydrogen bonds : angle 3.97994 ( 4260) covalent geometry : bond 0.00280 (24999) covalent geometry : angle 0.50204 (33895) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1448 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8138 (t0) REVERT: A 1847 ASP cc_start: 0.8327 (t0) cc_final: 0.7971 (t0) REVERT: A 1849 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8093 (mmtt) REVERT: A 2129 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7705 (tp30) REVERT: A 2169 GLN cc_start: 0.7654 (pm20) cc_final: 0.6692 (mm-40) REVERT: A 2438 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7561 (mt-10) REVERT: A 2610 ARG cc_start: 0.8024 (ttm110) cc_final: 0.7287 (mtm110) REVERT: A 2615 MET cc_start: 0.8891 (mmt) cc_final: 0.8405 (mmt) REVERT: A 2671 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7635 (mtt) REVERT: A 2793 ILE cc_start: 0.8690 (pt) cc_final: 0.8457 (mt) REVERT: A 2863 ARG cc_start: 0.7623 (tmt170) cc_final: 0.7372 (tmt170) REVERT: A 2879 LYS cc_start: 0.8391 (tppt) cc_final: 0.7543 (ttpp) REVERT: A 3117 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7621 (tttt) REVERT: A 3167 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7479 (mtm-85) REVERT: A 3202 ASN cc_start: 0.7429 (t0) cc_final: 0.6989 (m-40) REVERT: A 3499 GLN cc_start: 0.8387 (mt0) cc_final: 0.8058 (tp40) REVERT: A 3537 GLN cc_start: 0.8314 (tt0) cc_final: 0.8036 (tp40) REVERT: A 3655 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7726 (mtp85) REVERT: A 3668 ASP cc_start: 0.7158 (p0) cc_final: 0.6742 (p0) REVERT: A 3683 ASP cc_start: 0.8804 (t0) cc_final: 0.8543 (t0) REVERT: A 3737 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: A 4581 ILE cc_start: 0.8238 (mt) cc_final: 0.7955 (mp) outliers start: 68 outliers final: 60 residues processed: 331 average time/residue: 0.3635 time to fit residues: 193.8205 Evaluate side-chains 337 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 272 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2281 THR Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2521 ILE Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2626 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2761 SER Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3117 LYS Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3655 ARG Chi-restraints excluded: chain A residue 3661 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3737 GLU Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3780 VAL Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 4012 ASN Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4293 ASP Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4468 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 70 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 207 optimal weight: 0.3980 chunk 189 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.148053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112948 restraints weight = 32850.692| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.52 r_work: 0.3209 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24999 Z= 0.121 Angle : 0.505 9.600 33895 Z= 0.249 Chirality : 0.038 0.185 3806 Planarity : 0.004 0.041 4343 Dihedral : 4.922 89.056 3348 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.56 % Allowed : 18.29 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.16), residues: 3019 helix: 2.27 (0.12), residues: 1812 sheet: -1.40 (0.34), residues: 214 loop : 0.19 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1435 HIS 0.008 0.001 HIS A3200 PHE 0.029 0.001 PHE A3004 TYR 0.017 0.001 TYR A2748 ARG 0.003 0.000 ARG A1488 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 1458) hydrogen bonds : angle 3.96830 ( 4260) covalent geometry : bond 0.00284 (24999) covalent geometry : angle 0.50477 (33895) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 277 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1448 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8123 (t0) REVERT: A 1488 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7886 (ttm110) REVERT: A 1847 ASP cc_start: 0.8346 (t0) cc_final: 0.7982 (t0) REVERT: A 1849 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8109 (mmtt) REVERT: A 2129 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7726 (tp30) REVERT: A 2169 GLN cc_start: 0.7672 (pm20) cc_final: 0.6728 (mm-40) REVERT: A 2180 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7032 (mp0) REVERT: A 2217 ASN cc_start: 0.6760 (m110) cc_final: 0.6557 (m-40) REVERT: A 2313 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 2438 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7528 (mt-10) REVERT: A 2610 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7475 (mtm180) REVERT: A 2615 MET cc_start: 0.8872 (mmt) cc_final: 0.8374 (mmt) REVERT: A 2671 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7577 (mtt) REVERT: A 2786 GLN cc_start: 0.8039 (mt0) cc_final: 0.7831 (mt0) REVERT: A 2793 ILE cc_start: 0.8685 (pt) cc_final: 0.8372 (mt) REVERT: A 2863 ARG cc_start: 0.7680 (tmt170) cc_final: 0.7379 (tmt170) REVERT: A 2879 LYS cc_start: 0.8389 (tppt) cc_final: 0.7546 (ttpp) REVERT: A 3167 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7457 (mtm-85) REVERT: A 3202 ASN cc_start: 0.7538 (t0) cc_final: 0.7042 (m-40) REVERT: A 3499 GLN cc_start: 0.8377 (mt0) cc_final: 0.8051 (tp40) REVERT: A 3537 GLN cc_start: 0.8274 (tt0) cc_final: 0.8008 (tp40) REVERT: A 3655 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7718 (mtp85) REVERT: A 3668 ASP cc_start: 0.7147 (p0) cc_final: 0.6756 (p0) REVERT: A 3683 ASP cc_start: 0.8796 (t0) cc_final: 0.8538 (t0) REVERT: A 3737 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: A 3910 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7710 (mtp180) REVERT: A 4295 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8192 (mm-40) REVERT: A 4581 ILE cc_start: 0.8223 (mt) cc_final: 0.7945 (mp) outliers start: 69 outliers final: 59 residues processed: 328 average time/residue: 0.3589 time to fit residues: 187.7700 Evaluate side-chains 331 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 267 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2281 THR Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2521 ILE Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2626 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2761 SER Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3655 ARG Chi-restraints excluded: chain A residue 3661 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3697 THR Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3737 GLU Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 4012 ASN Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4293 ASP Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 42 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 242 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108773 restraints weight = 33207.560| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.58 r_work: 0.3185 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24999 Z= 0.167 Angle : 0.535 10.446 33895 Z= 0.266 Chirality : 0.039 0.189 3806 Planarity : 0.004 0.042 4343 Dihedral : 4.988 91.175 3348 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.60 % Allowed : 18.18 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.16), residues: 3019 helix: 2.16 (0.12), residues: 1812 sheet: -1.47 (0.35), residues: 208 loop : 0.10 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A1435 HIS 0.005 0.001 HIS A4389 PHE 0.017 0.002 PHE A3813 TYR 0.021 0.001 TYR A2748 ARG 0.010 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1458) hydrogen bonds : angle 4.06361 ( 4260) covalent geometry : bond 0.00403 (24999) covalent geometry : angle 0.53538 (33895) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1448 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8139 (t0) REVERT: A 1488 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7862 (ttm110) REVERT: A 1831 ASP cc_start: 0.8082 (t0) cc_final: 0.7825 (t0) REVERT: A 1847 ASP cc_start: 0.8349 (t0) cc_final: 0.8007 (t0) REVERT: A 2129 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7716 (tp30) REVERT: A 2169 GLN cc_start: 0.7723 (pm20) cc_final: 0.6813 (mm-40) REVERT: A 2438 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7557 (mt-10) REVERT: A 2508 LEU cc_start: 0.7822 (pp) cc_final: 0.7591 (pt) REVERT: A 2610 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7493 (mtm180) REVERT: A 2615 MET cc_start: 0.8873 (mmt) cc_final: 0.8333 (mmt) REVERT: A 2671 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7563 (mtt) REVERT: A 2704 GLU cc_start: 0.7355 (tt0) cc_final: 0.6992 (tm-30) REVERT: A 2879 LYS cc_start: 0.8414 (tppt) cc_final: 0.7573 (ttpp) REVERT: A 3167 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7498 (mtm-85) REVERT: A 3499 GLN cc_start: 0.8393 (mt0) cc_final: 0.8064 (tp40) REVERT: A 3537 GLN cc_start: 0.8279 (tt0) cc_final: 0.8033 (tp40) REVERT: A 3655 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7867 (mtp85) REVERT: A 3668 ASP cc_start: 0.7175 (p0) cc_final: 0.6769 (p0) REVERT: A 3683 ASP cc_start: 0.8775 (t0) cc_final: 0.8505 (t0) REVERT: A 3737 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: A 4259 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7580 (tm-30) outliers start: 70 outliers final: 60 residues processed: 325 average time/residue: 0.3763 time to fit residues: 194.8183 Evaluate side-chains 331 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 267 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1448 ASP Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1667 ASN Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1767 SER Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1935 THR Chi-restraints excluded: chain A residue 2096 VAL Chi-restraints excluded: chain A residue 2161 LEU Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2281 THR Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2521 ILE Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2626 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2699 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2761 SER Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 2998 ASN Chi-restraints excluded: chain A residue 3097 TRP Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3122 VAL Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3655 ARG Chi-restraints excluded: chain A residue 3661 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3685 THR Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3737 GLU Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3749 LEU Chi-restraints excluded: chain A residue 3818 LEU Chi-restraints excluded: chain A residue 3900 THR Chi-restraints excluded: chain A residue 4012 ASN Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4166 VAL Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4275 THR Chi-restraints excluded: chain A residue 4288 VAL Chi-restraints excluded: chain A residue 4293 ASP Chi-restraints excluded: chain A residue 4295 GLN Chi-restraints excluded: chain A residue 4300 ILE Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4618 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 50 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 263 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 256 optimal weight: 0.7980 chunk 204 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3754 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.148375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111762 restraints weight = 33723.742| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.62 r_work: 0.3203 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24999 Z= 0.129 Angle : 0.514 11.245 33895 Z= 0.255 Chirality : 0.038 0.210 3806 Planarity : 0.004 0.042 4343 Dihedral : 4.916 88.175 3348 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.52 % Allowed : 18.62 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.16), residues: 3019 helix: 2.23 (0.12), residues: 1813 sheet: -1.40 (0.35), residues: 208 loop : 0.11 (0.21), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP A4478 HIS 0.005 0.001 HIS A4389 PHE 0.033 0.001 PHE A4410 TYR 0.017 0.001 TYR A2748 ARG 0.003 0.000 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 1458) hydrogen bonds : angle 3.99786 ( 4260) covalent geometry : bond 0.00303 (24999) covalent geometry : angle 0.51397 (33895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11493.35 seconds wall clock time: 200 minutes 1.87 seconds (12001.87 seconds total)