Starting phenix.real_space_refine on Fri May 23 21:05:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm8_44691/05_2025/9bm8_44691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm8_44691/05_2025/9bm8_44691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bm8_44691/05_2025/9bm8_44691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm8_44691/05_2025/9bm8_44691.map" model { file = "/net/cci-nas-00/data/ceres_data/9bm8_44691/05_2025/9bm8_44691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm8_44691/05_2025/9bm8_44691.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 120 5.16 5 C 15419 2.51 5 N 4182 2.21 5 O 4489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24220 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2991, 24104 Classifications: {'peptide': 2991} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 132, 'TRANS': 2858} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'ADP': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 13.38, per 1000 atoms: 0.55 Number of scatterers: 24220 At special positions: 0 Unit cell: (170.56, 149.76, 127.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 10 15.00 O 4489 8.00 N 4182 7.00 C 15419 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: 7.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5698 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 19 sheets defined 62.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 Processing helix chain 'A' and resid 1350 through 1354 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 Processing helix chain 'A' and resid 1396 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.568A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1472 Processing helix chain 'A' and resid 1489 through 1509 Processing helix chain 'A' and resid 1510 through 1515 removed outlier: 3.507A pdb=" N TYR A1513 " --> pdb=" O SER A1510 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1553 removed outlier: 3.636A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A1553 " --> pdb=" O GLY A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 Processing helix chain 'A' and resid 1561 through 1584 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1631 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.796A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1777 through 1797 removed outlier: 3.573A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1824 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 4.288A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1985 Processing helix chain 'A' and resid 2045 through 2057 removed outlier: 3.877A pdb=" N GLN A2051 " --> pdb=" O GLN A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2113 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.367A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2177 through 2189 removed outlier: 4.049A pdb=" N GLU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A2183 " --> pdb=" O ARG A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2230 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 3.572A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2365 through 2369 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.821A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2502 removed outlier: 3.662A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.750A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.913A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2601 through 2612 removed outlier: 3.815A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.043A 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 Processing helix chain 'A' and resid 2757 through 2764 Proline residue: A2760 - end of helix removed outlier: 3.630A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2757 through 2764' Processing helix chain 'A' and resid 2765 through 2783 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.839A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2885 through 2903 Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.504A pdb=" N GLN A2928 " --> pdb=" O ARG A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3006 through 3015 removed outlier: 3.549A pdb=" N LEU A3011 " --> pdb=" O ARG A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3021 Processing helix chain 'A' and resid 3022 through 3041 Processing helix chain 'A' and resid 3046 through 3062 Processing helix chain 'A' and resid 3084 through 3089 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.500A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3472 through 3502 Processing helix chain 'A' and resid 3503 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.547A pdb=" N TYR A3552 " --> pdb=" O ALA A3548 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3548 through 3553' Processing helix chain 'A' and resid 3555 through 3565 removed outlier: 3.573A pdb=" N ARG A3559 " --> pdb=" O ASN A3555 " (cutoff:3.500A) Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.530A pdb=" N TYR A3604 " --> pdb=" O ILE A3600 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3629 removed outlier: 3.737A pdb=" N PHE A3629 " --> pdb=" O SER A3625 " (cutoff:3.500A) Processing helix chain 'A' and resid 3637 through 3641 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3695 removed outlier: 3.773A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) 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 3757 Processing helix chain 'A' and resid 3762 through 3786 Processing helix chain 'A' and resid 3786 through 3818 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.615A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.708A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.200A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.539A 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 Processing helix chain 'A' and resid 3981 through 3996 Processing helix chain 'A' and resid 3997 through 3999 No H-bonds generated for 'chain 'A' and resid 3997 through 3999' Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.547A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4027 through 4033 Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.883A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4091 removed outlier: 4.045A pdb=" N ASN A4078 " --> pdb=" O ALA A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4114 Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.673A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4193 removed outlier: 4.133A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4194 through 4196 No H-bonds generated for 'chain 'A' and resid 4194 through 4196' Processing helix chain 'A' and resid 4197 through 4202 removed outlier: 3.651A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A4202 " --> pdb=" O PRO A4198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4197 through 4202' Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.539A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 removed outlier: 3.543A pdb=" N GLN A4262 " --> pdb=" O ASN A4258 " (cutoff:3.500A) Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.504A pdb=" N PHE A4278 " --> pdb=" O THR A4275 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.605A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4321 Processing helix chain 'A' and resid 4325 through 4346 removed outlier: 4.243A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4407 through 4439 removed outlier: 3.513A pdb=" N GLU A4439 " --> pdb=" O VAL A4435 " (cutoff:3.500A) Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4461 through 4465 Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4501 through 4506 removed outlier: 3.809A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4501 through 4506' Processing helix chain 'A' and resid 4516 through 4531 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 removed outlier: 3.575A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.712A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 10.425A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.460A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.365A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.109A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2253 Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2621 removed outlier: 6.330A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2642 removed outlier: 3.847A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.131A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.338A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3661 through 3664 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4067 removed outlier: 6.682A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 3.754A pdb=" N ALA A4285 " --> pdb=" O ILE A4294 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.666A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.735A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1406 hydrogen bonds defined for protein. 4107 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: 15.04 Time building geometry restraints manager: 7.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7946 1.34 - 1.46: 5223 1.46 - 1.58: 11358 1.58 - 1.70: 14 1.70 - 1.82: 202 Bond restraints: 24743 Sorted by residual: bond pdb=" N PHE A1462 " pdb=" CA PHE A1462 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.95e+00 bond pdb=" N GLN A1465 " pdb=" CA GLN A1465 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.16e-02 7.43e+03 5.53e+00 bond pdb=" N LEU A1459 " pdb=" CA LEU A1459 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.45e+00 bond pdb=" C SER A4172 " pdb=" N PRO A4173 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.27e-02 6.20e+03 5.27e+00 bond pdb=" N GLU A1460 " pdb=" CA GLU A1460 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.17e+00 ... (remaining 24738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 32807 1.65 - 3.30: 600 3.30 - 4.96: 96 4.96 - 6.61: 41 6.61 - 8.26: 13 Bond angle restraints: 33557 Sorted by residual: angle pdb=" C TYR A3125 " pdb=" CA TYR A3125 " pdb=" CB TYR A3125 " ideal model delta sigma weight residual 116.63 109.82 6.81 1.16e+00 7.43e-01 3.45e+01 angle pdb=" N ILE A4300 " pdb=" CA ILE A4300 " pdb=" C ILE A4300 " ideal model delta sigma weight residual 113.71 109.30 4.41 9.50e-01 1.11e+00 2.15e+01 angle pdb=" CA TYR A3125 " pdb=" C TYR A3125 " pdb=" N MET A3126 " ideal model delta sigma weight residual 119.63 116.21 3.42 8.10e-01 1.52e+00 1.78e+01 angle pdb=" C ASP A1933 " pdb=" N GLU A1934 " pdb=" CA GLU A1934 " ideal model delta sigma weight residual 121.54 128.43 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N MET A1507 " pdb=" CA MET A1507 " pdb=" CB MET A1507 " ideal model delta sigma weight residual 110.28 115.77 -5.49 1.55e+00 4.16e-01 1.25e+01 ... (remaining 33552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13482 17.99 - 35.98: 1222 35.98 - 53.97: 214 53.97 - 71.96: 78 71.96 - 89.95: 23 Dihedral angle restraints: 15019 sinusoidal: 6254 harmonic: 8765 Sorted by residual: dihedral pdb=" CA MET A3068 " pdb=" C MET A3068 " pdb=" N ASN A3069 " pdb=" CA ASN A3069 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 9.74 -69.73 1 2.00e+01 2.50e-03 1.57e+01 dihedral pdb=" CA TYR A2901 " pdb=" C TYR A2901 " pdb=" N GLU A2902 " pdb=" CA GLU A2902 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 15016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2664 0.036 - 0.071: 765 0.071 - 0.107: 277 0.107 - 0.142: 59 0.142 - 0.178: 7 Chirality restraints: 3772 Sorted by residual: chirality pdb=" CB THR A4315 " pdb=" CA THR A4315 " pdb=" OG1 THR A4315 " pdb=" CG2 THR A4315 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.90e-01 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 2.47 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CG LEU A2605 " pdb=" CB LEU A2605 " pdb=" CD1 LEU A2605 " pdb=" CD2 LEU A2605 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 3769 not shown) Planarity restraints: 4284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A3489 " 0.010 2.00e-02 2.50e+03 1.87e-02 8.76e+00 pdb=" CG TRP A3489 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A3489 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A3489 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A3489 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A3489 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A3489 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A3489 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP A3489 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A3489 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A3006 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C GLU A3006 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU A3006 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A3007 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A4172 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A4173 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A4173 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A4173 " 0.027 5.00e-02 4.00e+02 ... (remaining 4281 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 35 2.35 - 2.99: 12431 2.99 - 3.63: 37881 3.63 - 4.26: 55615 4.26 - 4.90: 94113 Nonbonded interactions: 200075 Sorted by model distance: nonbonded pdb=" CD1 LEU A1451 " pdb=" CG2 THR A3656 " model vdw 1.716 3.880 nonbonded pdb=" OD1 ASP A1448 " pdb=" CA GLY A3657 " model vdw 1.978 3.440 nonbonded pdb=" OD1 ASN A2752 " pdb=" OG1 THR A2770 " model vdw 2.183 3.040 nonbonded pdb=" OE1 GLU A2665 " pdb=" NH1 ARG A2720 " model vdw 2.207 3.120 nonbonded pdb=" O GLU A1548 " pdb=" OG1 THR A1552 " model vdw 2.223 3.040 ... (remaining 200070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 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: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 60.900 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24743 Z= 0.143 Angle : 0.588 8.259 33557 Z= 0.315 Chirality : 0.040 0.178 3772 Planarity : 0.004 0.047 4284 Dihedral : 14.752 89.951 9321 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 0.04 % Allowed : 0.79 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.16), residues: 2977 helix: 2.27 (0.13), residues: 1687 sheet: -0.96 (0.34), residues: 247 loop : 0.01 (0.21), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A3489 HIS 0.008 0.001 HIS A1810 PHE 0.026 0.001 PHE A1938 TYR 0.024 0.001 TYR A2582 ARG 0.009 0.001 ARG A3191 Details of bonding type rmsd hydrogen bonds : bond 0.12807 ( 1406) hydrogen bonds : angle 5.38005 ( 4107) covalent geometry : bond 0.00289 (24743) covalent geometry : angle 0.58804 (33557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.4660 (mmm) cc_final: 0.3900 (mmm) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.3634 time to fit residues: 177.5380 Evaluate side-chains 221 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 234 optimal weight: 0.0060 chunk 90 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2560 HIS ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3069 ASN A3602 ASN A3709 GLN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4453 ASN A4506 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.155145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107914 restraints weight = 38035.039| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.92 r_work: 0.3183 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24743 Z= 0.141 Angle : 0.554 11.665 33557 Z= 0.280 Chirality : 0.040 0.223 3772 Planarity : 0.004 0.050 4284 Dihedral : 6.728 89.945 3339 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.62 % Rotamer: Outliers : 1.39 % Allowed : 6.30 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.16), residues: 2977 helix: 2.23 (0.13), residues: 1721 sheet: -0.62 (0.33), residues: 256 loop : 0.05 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A3489 HIS 0.016 0.001 HIS A2560 PHE 0.032 0.001 PHE A1938 TYR 0.017 0.001 TYR A4447 ARG 0.008 0.000 ARG A3628 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 1406) hydrogen bonds : angle 4.39175 ( 4107) covalent geometry : bond 0.00319 (24743) covalent geometry : angle 0.55359 (33557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2221 MET cc_start: 0.8704 (ttp) cc_final: 0.8476 (ttm) REVERT: A 2263 HIS cc_start: 0.9051 (m170) cc_final: 0.8838 (m90) REVERT: A 2603 MET cc_start: 0.7414 (tmm) cc_final: 0.7034 (ttp) REVERT: A 2834 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8001 (tm-30) REVERT: A 3500 MET cc_start: 0.7552 (tpp) cc_final: 0.7294 (tpp) REVERT: A 3507 CYS cc_start: 0.8312 (m) cc_final: 0.7687 (m) REVERT: A 3571 ASP cc_start: 0.6893 (t0) cc_final: 0.6630 (t0) REVERT: A 3595 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8109 (mp10) REVERT: A 4117 GLN cc_start: 0.4269 (mm-40) cc_final: 0.3907 (mm-40) REVERT: A 4454 GLU cc_start: 0.7511 (tt0) cc_final: 0.7156 (tt0) REVERT: A 4459 ILE cc_start: 0.7893 (mp) cc_final: 0.7517 (mp) outliers start: 37 outliers final: 22 residues processed: 289 average time/residue: 0.3625 time to fit residues: 167.5796 Evaluate side-chains 254 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 2152 GLU Chi-restraints excluded: chain A residue 2320 ASP Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2919 VAL Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4569 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 0.4980 chunk 210 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1541 GLN A1651 GLN A2560 HIS ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3119 ASN A3534 HIS A3537 GLN A3538 GLN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.150280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102199 restraints weight = 38090.707| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.92 r_work: 0.3094 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 24743 Z= 0.238 Angle : 0.608 8.645 33557 Z= 0.309 Chirality : 0.043 0.210 3772 Planarity : 0.004 0.046 4284 Dihedral : 6.783 89.819 3339 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.84 % Rotamer: Outliers : 1.65 % Allowed : 9.19 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.16), residues: 2977 helix: 2.04 (0.13), residues: 1717 sheet: -0.80 (0.33), residues: 256 loop : -0.01 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A2845 HIS 0.016 0.001 HIS A2560 PHE 0.022 0.002 PHE A3813 TYR 0.016 0.002 TYR A2748 ARG 0.011 0.001 ARG A3628 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 1406) hydrogen bonds : angle 4.35333 ( 4107) covalent geometry : bond 0.00572 (24743) covalent geometry : angle 0.60787 (33557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2213 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7975 (mp) REVERT: A 2581 LEU cc_start: 0.8052 (mp) cc_final: 0.7553 (mp) REVERT: A 2603 MET cc_start: 0.7501 (tmm) cc_final: 0.7048 (ttp) REVERT: A 2834 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 2962 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8131 (mmmt) REVERT: A 3167 ARG cc_start: 0.7949 (tpp-160) cc_final: 0.7512 (tpm170) REVERT: A 3500 MET cc_start: 0.7609 (tpp) cc_final: 0.7203 (tpp) REVERT: A 3551 GLU cc_start: 0.8036 (pm20) cc_final: 0.7692 (pm20) REVERT: A 4095 MET cc_start: 0.7653 (ttt) cc_final: 0.7353 (ttt) REVERT: A 4117 GLN cc_start: 0.4828 (mm-40) cc_final: 0.4258 (mm-40) REVERT: A 4281 GLU cc_start: 0.8397 (mp0) cc_final: 0.7420 (tp30) outliers start: 44 outliers final: 29 residues processed: 281 average time/residue: 0.3842 time to fit residues: 169.2306 Evaluate side-chains 252 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1795 SER Chi-restraints excluded: chain A residue 2130 ASN Chi-restraints excluded: chain A residue 2152 GLU Chi-restraints excluded: chain A residue 2213 ILE Chi-restraints excluded: chain A residue 2320 ASP Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3704 THR Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3792 GLN Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4569 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 266 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 267 optimal weight: 4.9990 chunk 237 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2560 HIS ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3602 ASN ** A4453 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 = 0.3939 r_free = 0.3939 target = 0.153588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106085 restraints weight = 38355.035| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.94 r_work: 0.3149 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24743 Z= 0.122 Angle : 0.520 9.743 33557 Z= 0.263 Chirality : 0.039 0.206 3772 Planarity : 0.004 0.057 4284 Dihedral : 6.573 88.264 3339 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 1.80 % Allowed : 10.95 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.16), residues: 2977 helix: 2.22 (0.13), residues: 1719 sheet: -0.67 (0.33), residues: 254 loop : 0.01 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.015 0.001 HIS A2560 PHE 0.016 0.001 PHE A3813 TYR 0.016 0.001 TYR A2748 ARG 0.006 0.000 ARG A1567 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1406) hydrogen bonds : angle 4.13466 ( 4107) covalent geometry : bond 0.00272 (24743) covalent geometry : angle 0.52042 (33557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1567 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7565 (ttm110) REVERT: A 2213 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 2221 MET cc_start: 0.8647 (ttp) cc_final: 0.8419 (ttm) REVERT: A 2603 MET cc_start: 0.7442 (tmm) cc_final: 0.7067 (ttp) REVERT: A 2834 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7759 (tm-30) REVERT: A 2959 TYR cc_start: 0.8323 (t80) cc_final: 0.7813 (t80) REVERT: A 2962 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8253 (mmmt) REVERT: A 3500 MET cc_start: 0.7574 (tpp) cc_final: 0.6934 (tpp) REVERT: A 3683 ASP cc_start: 0.7970 (t0) cc_final: 0.7572 (t0) REVERT: A 4095 MET cc_start: 0.7548 (ttt) cc_final: 0.7322 (ttt) REVERT: A 4117 GLN cc_start: 0.4806 (mm-40) cc_final: 0.4288 (mm-40) REVERT: A 4281 GLU cc_start: 0.8405 (mp0) cc_final: 0.7444 (tp30) REVERT: A 4304 GLU cc_start: 0.7301 (tp30) cc_final: 0.7055 (tp30) REVERT: A 4449 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7920 (mtm110) outliers start: 48 outliers final: 36 residues processed: 287 average time/residue: 0.3708 time to fit residues: 169.0802 Evaluate side-chains 265 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 2130 ASN Chi-restraints excluded: chain A residue 2213 ILE Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2320 ASP Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2919 VAL Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3792 GLN Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4389 HIS Chi-restraints excluded: chain A residue 4433 ASP Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4569 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 17 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 chunk 237 optimal weight: 0.8980 chunk 271 optimal weight: 0.8980 chunk 210 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4530 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.153774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106388 restraints weight = 38201.488| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.94 r_work: 0.3156 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24743 Z= 0.124 Angle : 0.520 9.076 33557 Z= 0.260 Chirality : 0.040 0.227 3772 Planarity : 0.004 0.057 4284 Dihedral : 6.443 89.770 3339 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 1.58 % Allowed : 11.85 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.16), residues: 2977 helix: 2.30 (0.12), residues: 1719 sheet: -0.76 (0.33), residues: 257 loop : 0.05 (0.21), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1701 HIS 0.006 0.001 HIS A2588 PHE 0.019 0.001 PHE A3094 TYR 0.017 0.001 TYR A2901 ARG 0.005 0.000 ARG A4449 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 1406) hydrogen bonds : angle 4.02653 ( 4107) covalent geometry : bond 0.00284 (24743) covalent geometry : angle 0.51962 (33557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1567 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7457 (ttm110) REVERT: A 2187 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8548 (tm-30) REVERT: A 2213 ILE cc_start: 0.8256 (mp) cc_final: 0.7878 (mp) REVERT: A 2308 ASP cc_start: 0.8196 (p0) cc_final: 0.7957 (p0) REVERT: A 2310 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7917 (pt0) REVERT: A 2603 MET cc_start: 0.7632 (tmm) cc_final: 0.7239 (ttp) REVERT: A 2959 TYR cc_start: 0.8241 (t80) cc_final: 0.7788 (t80) REVERT: A 2962 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8252 (mmmt) REVERT: A 3500 MET cc_start: 0.7416 (tpp) cc_final: 0.7183 (tpp) REVERT: A 3607 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7521 (mtp85) REVERT: A 3683 ASP cc_start: 0.7899 (t0) cc_final: 0.7511 (t0) REVERT: A 4095 MET cc_start: 0.7694 (ttt) cc_final: 0.7483 (ttt) REVERT: A 4117 GLN cc_start: 0.4860 (mm-40) cc_final: 0.4474 (mm-40) REVERT: A 4281 GLU cc_start: 0.8398 (mp0) cc_final: 0.7446 (tp30) REVERT: A 4304 GLU cc_start: 0.7300 (tp30) cc_final: 0.7043 (tp30) REVERT: A 4449 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7806 (mtm110) REVERT: A 4454 GLU cc_start: 0.7655 (tt0) cc_final: 0.7405 (tt0) outliers start: 42 outliers final: 37 residues processed: 279 average time/residue: 0.3738 time to fit residues: 168.2345 Evaluate side-chains 268 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 2174 GLU Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2320 ASP Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2606 PHE Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3792 GLN Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4389 HIS Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4569 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 293 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 chunk 141 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2554 GLN A2560 HIS ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2930 GLN A3631 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4453 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 = 0.3936 r_free = 0.3936 target = 0.153678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106601 restraints weight = 37783.584| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.91 r_work: 0.3150 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24743 Z= 0.137 Angle : 0.517 7.438 33557 Z= 0.259 Chirality : 0.039 0.177 3772 Planarity : 0.004 0.057 4284 Dihedral : 6.371 87.077 3339 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.52 % Favored : 97.45 % Rotamer: Outliers : 1.91 % Allowed : 12.27 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.16), residues: 2977 helix: 2.32 (0.13), residues: 1719 sheet: -0.77 (0.33), residues: 257 loop : 0.07 (0.21), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1701 HIS 0.012 0.001 HIS A2560 PHE 0.018 0.001 PHE A3813 TYR 0.013 0.001 TYR A2748 ARG 0.005 0.000 ARG A3628 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 1406) hydrogen bonds : angle 3.99846 ( 4107) covalent geometry : bond 0.00321 (24743) covalent geometry : angle 0.51654 (33557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 242 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1567 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7383 (ttm110) REVERT: A 2012 MET cc_start: 0.8887 (ptm) cc_final: 0.8547 (ttp) REVERT: A 2187 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8519 (tm-30) REVERT: A 2213 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 2308 ASP cc_start: 0.8215 (p0) cc_final: 0.7983 (p0) REVERT: A 2310 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7955 (pt0) REVERT: A 2603 MET cc_start: 0.7672 (tmm) cc_final: 0.7039 (ttp) REVERT: A 2959 TYR cc_start: 0.8364 (t80) cc_final: 0.7978 (t80) REVERT: A 2962 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8330 (mmmt) REVERT: A 3167 ARG cc_start: 0.7727 (tpp-160) cc_final: 0.7486 (tpp-160) REVERT: A 3607 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7559 (mtp85) REVERT: A 3683 ASP cc_start: 0.7967 (t0) cc_final: 0.7602 (t0) REVERT: A 4095 MET cc_start: 0.7780 (ttt) cc_final: 0.7431 (ttt) REVERT: A 4117 GLN cc_start: 0.4935 (mm-40) cc_final: 0.4529 (mm-40) REVERT: A 4281 GLU cc_start: 0.8400 (mp0) cc_final: 0.7469 (tp30) REVERT: A 4304 GLU cc_start: 0.7326 (tp30) cc_final: 0.7052 (tp30) REVERT: A 4449 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7848 (mtm110) outliers start: 51 outliers final: 37 residues processed: 278 average time/residue: 0.3682 time to fit residues: 163.6890 Evaluate side-chains 265 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 2130 ASN Chi-restraints excluded: chain A residue 2213 ILE Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2320 ASP Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3792 GLN Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4389 HIS Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4569 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 232 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2560 HIS A3200 HIS A3602 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103441 restraints weight = 38076.164| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.93 r_work: 0.3126 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24743 Z= 0.160 Angle : 0.540 11.836 33557 Z= 0.269 Chirality : 0.040 0.341 3772 Planarity : 0.004 0.054 4284 Dihedral : 6.355 88.162 3339 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 2.03 % Allowed : 13.13 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 2977 helix: 2.26 (0.12), residues: 1724 sheet: -0.82 (0.34), residues: 258 loop : 0.10 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1701 HIS 0.009 0.001 HIS A2560 PHE 0.019 0.001 PHE A3066 TYR 0.017 0.001 TYR A2748 ARG 0.006 0.000 ARG A3191 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 1406) hydrogen bonds : angle 4.02275 ( 4107) covalent geometry : bond 0.00380 (24743) covalent geometry : angle 0.53984 (33557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1567 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7407 (ttm110) REVERT: A 1613 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7311 (mmtt) REVERT: A 2012 MET cc_start: 0.8958 (ptm) cc_final: 0.8557 (ttp) REVERT: A 2187 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 2213 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7874 (mp) REVERT: A 2308 ASP cc_start: 0.8188 (p0) cc_final: 0.7977 (p0) REVERT: A 2310 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7919 (pt0) REVERT: A 2603 MET cc_start: 0.7616 (tmm) cc_final: 0.7366 (ttp) REVERT: A 2816 LEU cc_start: 0.8864 (tp) cc_final: 0.8622 (tp) REVERT: A 2959 TYR cc_start: 0.8256 (t80) cc_final: 0.7861 (t80) REVERT: A 2962 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8292 (mmmt) REVERT: A 3167 ARG cc_start: 0.7741 (tpp-160) cc_final: 0.7442 (tpp-160) REVERT: A 3551 GLU cc_start: 0.7706 (pm20) cc_final: 0.7500 (pm20) REVERT: A 3607 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7558 (mtp85) REVERT: A 3683 ASP cc_start: 0.8008 (t0) cc_final: 0.7633 (t0) REVERT: A 4095 MET cc_start: 0.7849 (ttt) cc_final: 0.7554 (ttt) REVERT: A 4117 GLN cc_start: 0.5061 (mm-40) cc_final: 0.4606 (mm-40) REVERT: A 4281 GLU cc_start: 0.8390 (mp0) cc_final: 0.7485 (tp30) REVERT: A 4304 GLU cc_start: 0.7380 (tp30) cc_final: 0.7091 (tp30) REVERT: A 4449 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7803 (mtm110) outliers start: 54 outliers final: 43 residues processed: 272 average time/residue: 0.3731 time to fit residues: 162.8217 Evaluate side-chains 268 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 2130 ASN Chi-restraints excluded: chain A residue 2213 ILE Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2320 ASP Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3068 MET Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3792 GLN Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4298 ASP Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4569 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 179 optimal weight: 0.9990 chunk 285 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2560 HIS A2849 ASN A2998 ASN A3631 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103384 restraints weight = 38135.340| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.94 r_work: 0.3125 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24743 Z= 0.153 Angle : 0.539 11.570 33557 Z= 0.269 Chirality : 0.040 0.286 3772 Planarity : 0.004 0.053 4284 Dihedral : 6.326 89.275 3339 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 1.84 % Allowed : 13.77 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.16), residues: 2977 helix: 2.28 (0.12), residues: 1716 sheet: -0.85 (0.33), residues: 258 loop : 0.07 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A2845 HIS 0.013 0.001 HIS A3200 PHE 0.021 0.001 PHE A3066 TYR 0.021 0.001 TYR A2748 ARG 0.005 0.000 ARG A3191 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 1406) hydrogen bonds : angle 4.02452 ( 4107) covalent geometry : bond 0.00364 (24743) covalent geometry : angle 0.53906 (33557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1567 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7395 (ttm110) REVERT: A 2012 MET cc_start: 0.8937 (ptm) cc_final: 0.8553 (ttp) REVERT: A 2187 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8402 (tm-30) REVERT: A 2213 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7915 (mp) REVERT: A 2308 ASP cc_start: 0.8205 (p0) cc_final: 0.7843 (p0) REVERT: A 2310 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7925 (pt0) REVERT: A 2603 MET cc_start: 0.7725 (tmm) cc_final: 0.7451 (ttp) REVERT: A 2845 TRP cc_start: 0.6292 (t60) cc_final: 0.5866 (t60) REVERT: A 2959 TYR cc_start: 0.8256 (t80) cc_final: 0.7872 (t80) REVERT: A 2962 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8326 (mmmt) REVERT: A 3167 ARG cc_start: 0.7766 (tpp-160) cc_final: 0.7461 (tpp-160) REVERT: A 3607 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7556 (mtp85) REVERT: A 3683 ASP cc_start: 0.7980 (t0) cc_final: 0.7615 (t0) REVERT: A 4095 MET cc_start: 0.7858 (ttt) cc_final: 0.7581 (ttt) REVERT: A 4117 GLN cc_start: 0.5217 (mm-40) cc_final: 0.4673 (mm-40) REVERT: A 4304 GLU cc_start: 0.7402 (tp30) cc_final: 0.7110 (tp30) REVERT: A 4449 ARG cc_start: 0.8112 (mtm110) cc_final: 0.7804 (mtm110) outliers start: 49 outliers final: 41 residues processed: 276 average time/residue: 0.3934 time to fit residues: 174.3299 Evaluate side-chains 267 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1795 SER Chi-restraints excluded: chain A residue 2130 ASN Chi-restraints excluded: chain A residue 2213 ILE Chi-restraints excluded: chain A residue 2287 ILE Chi-restraints excluded: chain A residue 2320 ASP Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3792 GLN Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4298 ASP Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4569 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 136 optimal weight: 0.0010 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.0040 chunk 98 optimal weight: 0.0070 chunk 206 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 276 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2485 GLN A2560 HIS A3200 HIS A3563 GLN A3602 ASN A3631 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.157100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109213 restraints weight = 37917.250| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.01 r_work: 0.3175 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 24743 Z= 0.107 Angle : 0.524 10.384 33557 Z= 0.260 Chirality : 0.039 0.230 3772 Planarity : 0.004 0.070 4284 Dihedral : 6.108 86.323 3339 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.21 % Rotamer: Outliers : 1.43 % Allowed : 14.33 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.16), residues: 2977 helix: 2.40 (0.13), residues: 1717 sheet: -0.76 (0.34), residues: 257 loop : 0.19 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2845 HIS 0.017 0.001 HIS A2560 PHE 0.016 0.001 PHE A3066 TYR 0.018 0.001 TYR A2748 ARG 0.010 0.000 ARG A3191 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 1406) hydrogen bonds : angle 3.91750 ( 4107) covalent geometry : bond 0.00229 (24743) covalent geometry : angle 0.52413 (33557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1567 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7381 (ttm110) REVERT: A 2187 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8511 (tm-30) REVERT: A 2213 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7913 (mp) REVERT: A 2308 ASP cc_start: 0.8212 (p0) cc_final: 0.7944 (p0) REVERT: A 2310 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7866 (pt0) REVERT: A 2517 TYR cc_start: 0.8103 (t80) cc_final: 0.7398 (t80) REVERT: A 2603 MET cc_start: 0.7735 (tmm) cc_final: 0.7451 (ttp) REVERT: A 2845 TRP cc_start: 0.6585 (t60) cc_final: 0.6325 (t60) REVERT: A 2959 TYR cc_start: 0.8328 (t80) cc_final: 0.7992 (t80) REVERT: A 2962 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8357 (mmmt) REVERT: A 3167 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7522 (tpp-160) REVERT: A 3607 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7462 (mtp85) REVERT: A 3683 ASP cc_start: 0.7921 (t0) cc_final: 0.7588 (t0) REVERT: A 4095 MET cc_start: 0.7801 (ttt) cc_final: 0.7526 (ttt) REVERT: A 4105 TRP cc_start: 0.8240 (t60) cc_final: 0.8010 (t60) REVERT: A 4117 GLN cc_start: 0.5116 (mm-40) cc_final: 0.4680 (mm-40) REVERT: A 4259 GLU cc_start: 0.8160 (tp30) cc_final: 0.7826 (tp30) REVERT: A 4281 GLU cc_start: 0.8380 (mp0) cc_final: 0.7539 (tp30) REVERT: A 4304 GLU cc_start: 0.7315 (tp30) cc_final: 0.7045 (tp30) REVERT: A 4449 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7856 (mtm110) outliers start: 38 outliers final: 31 residues processed: 276 average time/residue: 0.3614 time to fit residues: 158.9901 Evaluate side-chains 265 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1795 SER Chi-restraints excluded: chain A residue 2213 ILE Chi-restraints excluded: chain A residue 2320 ASP Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2879 LYS Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3200 HIS Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3792 GLN Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4569 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 185 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2560 HIS ** A2588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS A3631 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.153841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105695 restraints weight = 37959.370| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.91 r_work: 0.3163 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24743 Z= 0.123 Angle : 0.538 14.375 33557 Z= 0.266 Chirality : 0.040 0.217 3772 Planarity : 0.004 0.058 4284 Dihedral : 6.051 85.674 3339 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.14 % Rotamer: Outliers : 1.24 % Allowed : 14.67 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.16), residues: 2977 helix: 2.37 (0.12), residues: 1719 sheet: -0.71 (0.34), residues: 255 loop : 0.17 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A2845 HIS 0.016 0.001 HIS A3200 PHE 0.017 0.001 PHE A3813 TYR 0.018 0.001 TYR A2748 ARG 0.005 0.000 ARG A2684 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 1406) hydrogen bonds : angle 3.92591 ( 4107) covalent geometry : bond 0.00284 (24743) covalent geometry : angle 0.53850 (33557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1567 ARG cc_start: 0.7692 (ttm110) cc_final: 0.7387 (ttm110) REVERT: A 2187 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8478 (tm-30) REVERT: A 2213 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 2269 ASP cc_start: 0.6884 (m-30) cc_final: 0.6542 (m-30) REVERT: A 2308 ASP cc_start: 0.8147 (p0) cc_final: 0.7873 (p0) REVERT: A 2310 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7838 (pt0) REVERT: A 2517 TYR cc_start: 0.8033 (t80) cc_final: 0.7365 (t80) REVERT: A 2603 MET cc_start: 0.7697 (tmm) cc_final: 0.7399 (ttp) REVERT: A 2834 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 2959 TYR cc_start: 0.8313 (t80) cc_final: 0.7988 (t80) REVERT: A 2962 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8402 (mmmt) REVERT: A 3012 LEU cc_start: 0.3692 (mp) cc_final: 0.3464 (mp) REVERT: A 3167 ARG cc_start: 0.7759 (tpp-160) cc_final: 0.7438 (tpp-160) REVERT: A 3607 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7567 (mtp85) REVERT: A 3683 ASP cc_start: 0.7937 (t0) cc_final: 0.7572 (t0) REVERT: A 4095 MET cc_start: 0.7796 (ttt) cc_final: 0.7493 (ttt) REVERT: A 4117 GLN cc_start: 0.5101 (mm-40) cc_final: 0.4658 (mm-40) REVERT: A 4259 GLU cc_start: 0.8149 (tp30) cc_final: 0.7754 (tp30) REVERT: A 4281 GLU cc_start: 0.8350 (mp0) cc_final: 0.7487 (tp30) REVERT: A 4304 GLU cc_start: 0.7315 (tp30) cc_final: 0.7033 (tp30) REVERT: A 4449 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7835 (mtm110) outliers start: 33 outliers final: 31 residues processed: 257 average time/residue: 0.3590 time to fit residues: 147.6550 Evaluate side-chains 261 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1795 SER Chi-restraints excluded: chain A residue 2213 ILE Chi-restraints excluded: chain A residue 2320 ASP Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2499 LEU Chi-restraints excluded: chain A residue 2560 HIS Chi-restraints excluded: chain A residue 2907 VAL Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2939 SER Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3523 GLN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3792 GLN Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4218 THR Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4315 THR Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4569 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 89 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 107 optimal weight: 0.0020 chunk 256 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 91 optimal weight: 0.0030 chunk 161 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2560 HIS A3155 HIS A3200 HIS A3602 ASN A3631 ASN ** A4065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.154941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107991 restraints weight = 37757.091| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.89 r_work: 0.3164 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24743 Z= 0.111 Angle : 0.528 13.697 33557 Z= 0.261 Chirality : 0.039 0.199 3772 Planarity : 0.004 0.058 4284 Dihedral : 5.985 84.083 3339 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 1.50 % Allowed : 14.48 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.16), residues: 2977 helix: 2.39 (0.12), residues: 1719 sheet: -0.68 (0.34), residues: 245 loop : 0.19 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A2845 HIS 0.004 0.001 HIS A2791 PHE 0.021 0.001 PHE A2784 TYR 0.017 0.001 TYR A2748 ARG 0.004 0.000 ARG A2684 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1406) hydrogen bonds : angle 3.89817 ( 4107) covalent geometry : bond 0.00251 (24743) covalent geometry : angle 0.52770 (33557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12885.15 seconds wall clock time: 223 minutes 56.75 seconds (13436.75 seconds total)