Starting phenix.real_space_refine on Mon Aug 25 13:49:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0t_47370/08_2025/9e0t_47370.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0t_47370/08_2025/9e0t_47370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e0t_47370/08_2025/9e0t_47370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0t_47370/08_2025/9e0t_47370.map" model { file = "/net/cci-nas-00/data/ceres_data/9e0t_47370/08_2025/9e0t_47370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0t_47370/08_2025/9e0t_47370.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 151 5.16 5 C 17750 2.51 5 N 4844 2.21 5 O 5162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27918 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 22816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2892, 22816 Classifications: {'peptide': 2892} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PCIS': 4, 'PTRANS': 125, 'TRANS': 2762} Chain breaks: 13 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 30, 'ASP:plan': 13, 'ASN:plan1': 5, 'TYR:plan': 5, 'ARG:plan': 10, 'HIS:plan': 3, 'PHE:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 330 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "C" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.15, per 1000 atoms: 0.22 Number of scatterers: 27918 At special positions: 0 Unit cell: (111.265, 158.015, 198.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 151 16.00 P 9 15.00 Mg 2 11.99 O 5162 8.00 N 4844 7.00 C 17750 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: 2.26 Conformation dependent library (CDL) restraints added in 892.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 37 sheets defined 52.0% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 1444 through 1472 Processing helix chain 'A' and resid 1489 through 1510 removed outlier: 4.281A pdb=" N LEU A1493 " --> pdb=" O GLY A1489 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A1510 " --> pdb=" O ALA A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1515 removed outlier: 3.834A pdb=" N VAL A1515 " --> pdb=" O TYR A1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1512 through 1515' Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.845A pdb=" N ALA A1520 " --> pdb=" O PHE A1516 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.671A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1615 Processing helix chain 'A' and resid 1616 through 1624 removed outlier: 4.174A pdb=" N GLU A1620 " --> pdb=" O GLY A1616 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1632 removed outlier: 3.507A pdb=" N PHE A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1647 through 1652 removed outlier: 3.806A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.760A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.630A pdb=" N ARG A1710 " --> pdb=" O GLU A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1767 Processing helix chain 'A' and resid 1776 through 1797 Processing helix chain 'A' and resid 1801 through 1828 removed outlier: 3.745A pdb=" N SER A1828 " --> pdb=" O SER A1824 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1841 removed outlier: 4.473A pdb=" N GLN A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1912 through 1923 Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.815A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 3.542A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.770A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2114 removed outlier: 3.588A pdb=" N GLU A2114 " --> pdb=" O LYS A2110 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2311 through 2314 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2370 through 2384 removed outlier: 3.718A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2428 Proline residue: A2425 - end of helix Processing helix chain 'A' and resid 2432 through 2443 removed outlier: 3.566A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.780A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 4.184A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) removed outlier: 4.187A 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 2571 through 2587 removed outlier: 4.171A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.664A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2638 Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2739 through 2756 removed outlier: 4.120A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A2746 " --> pdb=" O ALA A2742 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2762 through 2764 No H-bonds generated for 'chain 'A' and resid 2762 through 2764' Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.504A pdb=" N ARG A2783 " --> pdb=" O MET A2779 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.814A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 4.083A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A2903 " --> pdb=" O VAL A2899 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.877A 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 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.840A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.738A pdb=" N ALA A3027 " --> pdb=" O GLY A3023 " (cutoff:3.500A) Processing helix chain 'A' and resid 3047 through 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 4.054A pdb=" N LYS A3076 " --> pdb=" O SER A3072 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 removed outlier: 3.553A pdb=" N GLY A3165 " --> pdb=" O LEU A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3240 removed outlier: 3.583A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3451 through 3500 removed outlier: 4.545A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG A3488 " --> pdb=" O ALA A3484 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A3491 " --> pdb=" O GLU A3487 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN A3498 " --> pdb=" O GLU A3494 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3517 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.658A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3616 through 3618 No H-bonds generated for 'chain 'A' and resid 3616 through 3618' Processing helix chain 'A' and resid 3619 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3755 Processing helix chain 'A' and resid 3759 through 3763 removed outlier: 3.883A pdb=" N ASP A3763 " --> pdb=" O ILE A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3764 through 3818 removed outlier: 4.297A pdb=" N VAL A3784 " --> pdb=" O VAL A3780 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU A3785 " --> pdb=" O THR A3781 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU A3786 " --> pdb=" O ARG A3782 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3840 removed outlier: 3.603A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.843A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3894 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 removed outlier: 3.990A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.977A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.677A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 Processing helix chain 'A' and resid 4073 through 4090 Processing helix chain 'A' and resid 4098 through 4101 removed outlier: 3.521A pdb=" N LEU A4101 " --> pdb=" O ASN A4098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4098 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 4.085A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) 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: 3.607A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4193 Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.599A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 removed outlier: 3.633A pdb=" N ILE A4238 " --> pdb=" O PRO A4235 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4252 through 4256 removed outlier: 3.855A pdb=" N ARG A4255 " --> pdb=" O TYR A4252 " (cutoff:3.500A) Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.785A pdb=" N PHE A4278 " --> pdb=" O THR A4274 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4324 through 4327 Processing helix chain 'A' and resid 4328 through 4348 Processing helix chain 'A' and resid 4380 through 4391 Processing helix chain 'A' and resid 4392 through 4395 Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4498 removed outlier: 3.645A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A4498 " --> pdb=" O LEU A4494 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.733A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4539 removed outlier: 3.789A pdb=" N GLU A4538 " --> pdb=" O SER A4535 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A4539 " --> pdb=" O LEU A4536 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4535 through 4539' Processing helix chain 'A' and resid 4631 through 4638 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.759A pdb=" N GLU B 93 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP B 94 " --> pdb=" O PRO B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 94' Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.794A pdb=" N SER B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.819A pdb=" N TRP C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.750A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 10.529A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.748A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.340A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1928 removed outlier: 6.776A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR A2017 " --> pdb=" O GLY A1955 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE A1957 " --> pdb=" O THR A2017 " (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 2000 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 7.441A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A2220 " --> pdb=" O PHE A2343 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL A2345 " --> pdb=" O LEU A2220 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N MET A2222 " --> pdb=" O VAL A2345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 3.520A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 4.230A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.229A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.337A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB8, first strand: chain 'A' and resid 4067 through 4070 removed outlier: 5.953A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 6.894A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS A4286 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS A4292 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4508 through 4510 Processing sheet with id=AC2, first strand: chain 'A' and resid 4564 through 4565 removed outlier: 8.097A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 4568 through 4570 Processing sheet with id=AC4, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.768A pdb=" N ILE B 95 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.768A pdb=" N ILE B 95 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER B 399 " --> pdb=" O THR B 403 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 111 through 116 removed outlier: 6.794A pdb=" N ALA B 126 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL B 114 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL B 124 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 144 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP B 136 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE B 142 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 153 through 157 removed outlier: 6.784A pdb=" N CYS B 168 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 156 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 166 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE B 174 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR B 187 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 176 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 195 through 199 removed outlier: 3.637A pdb=" N ALA B 199 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 209 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B 211 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 216 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 228 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 220 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS B 226 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 237 through 242 Processing sheet with id=AD1, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.702A pdb=" N GLY B 314 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE B 282 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 312 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TRP B 284 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE B 310 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET B 332 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASP B 324 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N CYS B 330 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 341 through 346 removed outlier: 4.215A pdb=" N ILE B 353 " --> pdb=" O TRP B 365 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 355 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 357 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS B 374 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.726A pdb=" N TYR C 102 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AD5, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.591A pdb=" N ALA C 126 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 114 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 124 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 127 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N THR C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP C 136 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE C 142 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 153 through 158 removed outlier: 6.776A pdb=" N CYS C 168 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE C 156 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA C 166 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE C 158 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU C 164 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE C 174 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR C 187 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU C 176 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 195 through 200 removed outlier: 3.610A pdb=" N ILE C 207 " --> pdb=" O TRP C 219 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 209 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 211 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N THR C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU C 220 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N CYS C 226 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 237 through 242 removed outlier: 6.728A pdb=" N CYS C 252 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL C 240 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA C 250 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU C 248 " --> pdb=" O PRO C 242 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 279 through 284 removed outlier: 4.443A pdb=" N THR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET C 332 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASP C 324 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N CYS C 330 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.505A pdb=" N LYS C 374 " --> pdb=" O VAL C 364 " (cutoff:3.500A) 1516 hydrogen bonds defined for protein. 4440 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: 9.13 Time building geometry restraints manager: 3.10 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: 9115 1.34 - 1.46: 5100 1.46 - 1.58: 14056 1.58 - 1.70: 12 1.70 - 1.82: 245 Bond restraints: 28528 Sorted by residual: bond pdb=" CA ILE A2154 " pdb=" CB ILE A2154 " ideal model delta sigma weight residual 1.539 1.550 -0.011 5.40e-03 3.43e+04 4.07e+00 bond pdb=" CD1 TYR A3836 " pdb=" CE1 TYR A3836 " ideal model delta sigma weight residual 1.382 1.336 0.046 3.00e-02 1.11e+03 2.32e+00 bond pdb=" CA PHE A3823 " pdb=" CB PHE A3823 " ideal model delta sigma weight residual 1.530 1.555 -0.025 1.69e-02 3.50e+03 2.11e+00 bond pdb=" C ARG A2869 " pdb=" N PRO A2870 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.77e+00 bond pdb=" CB TYR A3836 " pdb=" CG TYR A3836 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.20e-02 2.07e+03 1.77e+00 ... (remaining 28523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 37947 1.96 - 3.92: 658 3.92 - 5.89: 96 5.89 - 7.85: 25 7.85 - 9.81: 4 Bond angle restraints: 38730 Sorted by residual: angle pdb=" N LEU A2668 " pdb=" CA LEU A2668 " pdb=" C LEU A2668 " ideal model delta sigma weight residual 109.81 119.62 -9.81 2.21e+00 2.05e-01 1.97e+01 angle pdb=" C GLU A1964 " pdb=" N GLU A1965 " pdb=" CA GLU A1965 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C SER A2384 " pdb=" N ILE A2385 " pdb=" CA ILE A2385 " ideal model delta sigma weight residual 122.13 127.98 -5.85 1.85e+00 2.92e-01 1.00e+01 angle pdb=" N GLU A2808 " pdb=" CA GLU A2808 " pdb=" CB GLU A2808 " ideal model delta sigma weight residual 110.41 115.52 -5.11 1.68e+00 3.54e-01 9.26e+00 angle pdb=" C ALA A1506 " pdb=" N MET A1507 " pdb=" CA MET A1507 " ideal model delta sigma weight residual 122.38 116.95 5.43 1.81e+00 3.05e-01 9.01e+00 ... (remaining 38725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.05: 15603 20.05 - 40.09: 1360 40.09 - 60.14: 157 60.14 - 80.18: 45 80.18 - 100.23: 11 Dihedral angle restraints: 17176 sinusoidal: 6892 harmonic: 10284 Sorted by residual: dihedral pdb=" O2A ADP A4806 " pdb=" O3A ADP A4806 " pdb=" PA ADP A4806 " pdb=" PB ADP A4806 " ideal model delta sinusoidal sigma weight residual -60.00 40.23 -100.23 1 2.00e+01 2.50e-03 2.83e+01 dihedral pdb=" O1B ADP A4806 " pdb=" O3A ADP A4806 " pdb=" PB ADP A4806 " pdb=" PA ADP A4806 " ideal model delta sinusoidal sigma weight residual -60.00 37.39 -97.39 1 2.00e+01 2.50e-03 2.71e+01 dihedral pdb=" CA MET B 201 " pdb=" C MET B 201 " pdb=" N PRO B 202 " pdb=" CA PRO B 202 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 17173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3861 0.069 - 0.138: 509 0.138 - 0.207: 25 0.207 - 0.277: 2 0.277 - 0.346: 1 Chirality restraints: 4398 Sorted by residual: chirality pdb=" CG LEU A3745 " pdb=" CB LEU A3745 " pdb=" CD1 LEU A3745 " pdb=" CD2 LEU A3745 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB ILE A4020 " pdb=" CA ILE A4020 " pdb=" CG1 ILE A4020 " pdb=" CG2 ILE A4020 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE A2385 " pdb=" CA ILE A2385 " pdb=" CG1 ILE A2385 " pdb=" CG2 ILE A2385 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 4395 not shown) Planarity restraints: 4929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A2584 " 0.024 2.00e-02 2.50e+03 1.98e-02 9.82e+00 pdb=" CG TRP A2584 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A2584 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A2584 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A2584 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A2584 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A2584 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2584 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2584 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A2584 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2668 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A2669 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A2669 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A2669 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1510 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO A1511 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1511 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1511 " 0.025 5.00e-02 4.00e+02 ... (remaining 4926 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 34 2.35 - 2.99: 13281 2.99 - 3.63: 42715 3.63 - 4.26: 63060 4.26 - 4.90: 107366 Nonbonded interactions: 226456 Sorted by model distance: nonbonded pdb=" OG SER A2231 " pdb=" OE2 GLU A2344 " model vdw 1.717 3.040 nonbonded pdb=" O1G ATP A4803 " pdb="MG MG A4804 " model vdw 1.997 2.170 nonbonded pdb=" O2B ADP A4801 " pdb="MG MG A4802 " model vdw 2.001 2.170 nonbonded pdb=" OD1 ASP A1958 " pdb="MG MG A4802 " model vdw 2.039 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4804 " model vdw 2.044 2.170 ... (remaining 226451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.710 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 28.950 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 0.046 28528 Z= 0.148 Angle : 0.644 9.812 38730 Z= 0.331 Chirality : 0.045 0.346 4398 Planarity : 0.005 0.060 4929 Dihedral : 14.858 100.227 10480 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 3482 helix: 1.07 (0.12), residues: 1676 sheet: -0.22 (0.25), residues: 461 loop : -0.91 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1467 TYR 0.021 0.001 TYR A1546 PHE 0.031 0.002 PHE A1945 TRP 0.050 0.001 TRP A2584 HIS 0.013 0.001 HIS A2560 Details of bonding type rmsd covalent geometry : bond 0.00316 (28528) covalent geometry : angle 0.64424 (38730) hydrogen bonds : bond 0.12286 ( 1513) hydrogen bonds : angle 5.92925 ( 4440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7362 (p0) cc_final: 0.6813 (t70) REVERT: A 1495 ASN cc_start: 0.8885 (m-40) cc_final: 0.8477 (m-40) REVERT: A 1564 GLU cc_start: 0.7726 (mm-30) cc_final: 0.6857 (mp0) REVERT: A 1646 ASN cc_start: 0.8871 (t0) cc_final: 0.8376 (t0) REVERT: A 1649 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8325 (mttt) REVERT: A 1872 TYR cc_start: 0.8342 (t80) cc_final: 0.8051 (t80) REVERT: A 1958 ASP cc_start: 0.6917 (t70) cc_final: 0.6630 (t70) REVERT: A 1967 MET cc_start: 0.8721 (tpp) cc_final: 0.8209 (mmm) REVERT: A 2018 MET cc_start: 0.8843 (mtm) cc_final: 0.8391 (mtm) REVERT: A 2239 LYS cc_start: 0.8333 (mtpp) cc_final: 0.7656 (mptt) REVERT: A 2479 PHE cc_start: 0.8122 (m-80) cc_final: 0.7871 (m-80) REVERT: A 2555 ILE cc_start: 0.7493 (tp) cc_final: 0.7015 (pt) REVERT: A 2699 THR cc_start: 0.8677 (m) cc_final: 0.8058 (p) REVERT: A 2851 ASP cc_start: 0.8736 (m-30) cc_final: 0.8349 (m-30) REVERT: A 3076 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8319 (mtpt) REVERT: A 3077 ASP cc_start: 0.7954 (t70) cc_final: 0.7731 (t0) REVERT: A 3108 GLU cc_start: 0.8750 (tp30) cc_final: 0.8369 (tp30) REVERT: A 3119 ASN cc_start: 0.8986 (t0) cc_final: 0.8486 (p0) REVERT: A 3621 LYS cc_start: 0.7843 (tmtt) cc_final: 0.7487 (tptp) REVERT: A 3669 ILE cc_start: 0.7509 (mt) cc_final: 0.7207 (mm) REVERT: A 3789 ILE cc_start: 0.7659 (tp) cc_final: 0.7450 (pt) REVERT: A 3902 ASP cc_start: 0.8081 (m-30) cc_final: 0.7699 (p0) REVERT: A 4022 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7199 (mp0) REVERT: A 4107 MET cc_start: 0.7439 (mmm) cc_final: 0.7206 (mmt) REVERT: A 4225 ASP cc_start: 0.8704 (t0) cc_final: 0.8462 (t0) REVERT: A 4295 GLN cc_start: 0.8526 (pt0) cc_final: 0.8070 (pm20) REVERT: A 4494 LEU cc_start: 0.8592 (tp) cc_final: 0.8379 (tt) REVERT: B 117 HIS cc_start: 0.7008 (t-90) cc_final: 0.6775 (t-90) REVERT: B 160 HIS cc_start: 0.7486 (t-90) cc_final: 0.6541 (p90) REVERT: B 218 MET cc_start: 0.6748 (tpp) cc_final: 0.5025 (mmt) REVERT: B 248 LEU cc_start: 0.7594 (tp) cc_final: 0.7336 (tp) REVERT: B 407 TRP cc_start: 0.5835 (m100) cc_final: 0.5191 (m100) REVERT: C 123 MET cc_start: 0.7475 (tmm) cc_final: 0.7177 (tmm) outliers start: 1 outliers final: 0 residues processed: 348 average time/residue: 0.1569 time to fit residues: 90.0781 Evaluate side-chains 259 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN A1976 GLN ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS A3854 GLN ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.136090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.096379 restraints weight = 48902.903| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.07 r_work: 0.3220 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28528 Z= 0.116 Angle : 0.544 8.443 38730 Z= 0.278 Chirality : 0.041 0.180 4398 Planarity : 0.004 0.050 4929 Dihedral : 5.459 102.242 3856 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.70 % Allowed : 8.12 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.14), residues: 3482 helix: 1.62 (0.13), residues: 1678 sheet: -0.34 (0.23), residues: 497 loop : -0.85 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1467 TYR 0.019 0.001 TYR A4049 PHE 0.012 0.001 PHE A1945 TRP 0.026 0.001 TRP B 340 HIS 0.006 0.001 HIS A2560 Details of bonding type rmsd covalent geometry : bond 0.00256 (28528) covalent geometry : angle 0.54437 (38730) hydrogen bonds : bond 0.03782 ( 1513) hydrogen bonds : angle 4.62843 ( 4440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 289 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7370 (p0) cc_final: 0.6850 (t70) REVERT: A 1495 ASN cc_start: 0.8851 (m-40) cc_final: 0.8638 (m-40) REVERT: A 1564 GLU cc_start: 0.7973 (mm-30) cc_final: 0.6998 (mp0) REVERT: A 1646 ASN cc_start: 0.8869 (t0) cc_final: 0.8536 (t0) REVERT: A 1649 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8346 (mttt) REVERT: A 1872 TYR cc_start: 0.8561 (t80) cc_final: 0.8302 (t80) REVERT: A 1958 ASP cc_start: 0.7105 (t70) cc_final: 0.6835 (t70) REVERT: A 1967 MET cc_start: 0.8729 (tpp) cc_final: 0.8230 (mmm) REVERT: A 2018 MET cc_start: 0.8855 (mtm) cc_final: 0.8348 (mtm) REVERT: A 2239 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7671 (mptt) REVERT: A 2479 PHE cc_start: 0.8176 (m-80) cc_final: 0.7888 (m-80) REVERT: A 2555 ILE cc_start: 0.7521 (tp) cc_final: 0.7030 (pt) REVERT: A 2699 THR cc_start: 0.8760 (m) cc_final: 0.8164 (p) REVERT: A 2785 THR cc_start: 0.8508 (t) cc_final: 0.8213 (p) REVERT: A 2851 ASP cc_start: 0.8749 (m-30) cc_final: 0.8372 (m-30) REVERT: A 3076 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8379 (mtpt) REVERT: A 3077 ASP cc_start: 0.8037 (t70) cc_final: 0.7827 (t0) REVERT: A 3104 GLN cc_start: 0.8821 (mt0) cc_final: 0.8513 (mt0) REVERT: A 3108 GLU cc_start: 0.8803 (tp30) cc_final: 0.8425 (tp30) REVERT: A 3621 LYS cc_start: 0.7943 (tmtt) cc_final: 0.7563 (tptp) REVERT: A 3676 VAL cc_start: 0.8918 (m) cc_final: 0.8713 (p) REVERT: A 3854 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7479 (pp30) REVERT: A 3902 ASP cc_start: 0.8070 (m-30) cc_final: 0.7758 (p0) REVERT: A 4022 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7227 (mp0) REVERT: A 4107 MET cc_start: 0.7493 (mmm) cc_final: 0.7227 (mmt) REVERT: A 4225 ASP cc_start: 0.8723 (t0) cc_final: 0.8475 (t0) REVERT: A 4295 GLN cc_start: 0.8615 (pt0) cc_final: 0.8207 (pm20) REVERT: A 4494 LEU cc_start: 0.8601 (tp) cc_final: 0.8400 (tt) REVERT: B 160 HIS cc_start: 0.7550 (t-90) cc_final: 0.6542 (p90) REVERT: B 201 MET cc_start: 0.7157 (pmm) cc_final: 0.5594 (ppp) REVERT: B 218 MET cc_start: 0.6945 (tpp) cc_final: 0.5207 (mpp) REVERT: B 219 TRP cc_start: 0.4155 (m-10) cc_final: 0.3479 (m100) REVERT: B 248 LEU cc_start: 0.7486 (tp) cc_final: 0.7145 (tt) REVERT: C 123 MET cc_start: 0.7523 (tmm) cc_final: 0.6989 (tmm) outliers start: 21 outliers final: 12 residues processed: 303 average time/residue: 0.1840 time to fit residues: 91.2195 Evaluate side-chains 270 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 257 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3854 GLN Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 111 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 347 optimal weight: 3.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3854 GLN ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS B 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096457 restraints weight = 48903.205| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.07 r_work: 0.3216 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28528 Z= 0.112 Angle : 0.524 8.766 38730 Z= 0.265 Chirality : 0.041 0.213 4398 Planarity : 0.004 0.048 4929 Dihedral : 5.302 102.513 3856 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.03 % Allowed : 10.60 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.14), residues: 3482 helix: 1.83 (0.13), residues: 1684 sheet: -0.36 (0.24), residues: 466 loop : -0.67 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2763 TYR 0.020 0.001 TYR A3836 PHE 0.012 0.001 PHE A1568 TRP 0.026 0.001 TRP B 261 HIS 0.013 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00252 (28528) covalent geometry : angle 0.52426 (38730) hydrogen bonds : bond 0.03555 ( 1513) hydrogen bonds : angle 4.36938 ( 4440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7357 (p0) cc_final: 0.6864 (t70) REVERT: A 1495 ASN cc_start: 0.8849 (m-40) cc_final: 0.8647 (m-40) REVERT: A 1646 ASN cc_start: 0.8868 (t0) cc_final: 0.8527 (t0) REVERT: A 1649 LYS cc_start: 0.8647 (mmtp) cc_final: 0.8386 (mttt) REVERT: A 1872 TYR cc_start: 0.8549 (t80) cc_final: 0.8265 (t80) REVERT: A 1958 ASP cc_start: 0.7121 (t70) cc_final: 0.6868 (t70) REVERT: A 1967 MET cc_start: 0.8701 (tpp) cc_final: 0.8063 (mmm) REVERT: A 2018 MET cc_start: 0.8833 (mtm) cc_final: 0.8310 (mtm) REVERT: A 2239 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7643 (mptt) REVERT: A 2479 PHE cc_start: 0.8191 (m-80) cc_final: 0.7896 (m-80) REVERT: A 2481 MET cc_start: 0.7602 (tpt) cc_final: 0.7323 (mmm) REVERT: A 2555 ILE cc_start: 0.7523 (tp) cc_final: 0.7030 (pt) REVERT: A 2699 THR cc_start: 0.8675 (m) cc_final: 0.8087 (p) REVERT: A 2785 THR cc_start: 0.8488 (t) cc_final: 0.8192 (p) REVERT: A 2836 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7668 (mtm-85) REVERT: A 2851 ASP cc_start: 0.8724 (m-30) cc_final: 0.8335 (m-30) REVERT: A 3076 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8357 (mtpt) REVERT: A 3077 ASP cc_start: 0.8041 (t70) cc_final: 0.7823 (t0) REVERT: A 3108 GLU cc_start: 0.8805 (tp30) cc_final: 0.8437 (tp30) REVERT: A 3621 LYS cc_start: 0.7932 (tmtt) cc_final: 0.7560 (tptp) REVERT: A 3669 ILE cc_start: 0.7402 (mm) cc_final: 0.7159 (mm) REVERT: A 3676 VAL cc_start: 0.8917 (m) cc_final: 0.8712 (p) REVERT: A 3854 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7230 (pp30) REVERT: A 3902 ASP cc_start: 0.8065 (m-30) cc_final: 0.7773 (p0) REVERT: A 4022 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7233 (mp0) REVERT: A 4092 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7604 (ptp-110) REVERT: A 4107 MET cc_start: 0.7467 (mmm) cc_final: 0.7227 (mmt) REVERT: A 4225 ASP cc_start: 0.8756 (t0) cc_final: 0.8499 (t0) REVERT: A 4295 GLN cc_start: 0.8592 (pt0) cc_final: 0.8184 (pm20) REVERT: B 102 TYR cc_start: 0.8338 (m-80) cc_final: 0.8120 (m-80) REVERT: B 201 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.5705 (ppp) REVERT: B 218 MET cc_start: 0.6904 (tpp) cc_final: 0.5450 (mpp) REVERT: B 219 TRP cc_start: 0.4165 (m-10) cc_final: 0.3445 (m100) REVERT: B 248 LEU cc_start: 0.7550 (tp) cc_final: 0.7224 (tt) REVERT: C 123 MET cc_start: 0.7437 (tmm) cc_final: 0.6857 (tmm) outliers start: 31 outliers final: 17 residues processed: 307 average time/residue: 0.1751 time to fit residues: 88.2891 Evaluate side-chains 280 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2808 GLU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3854 GLN Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4092 ARG Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 268 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 268 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 chunk 334 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 335 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 313 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2987 ASN ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094478 restraints weight = 48901.984| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.02 r_work: 0.3180 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28528 Z= 0.156 Angle : 0.553 12.364 38730 Z= 0.277 Chirality : 0.042 0.244 4398 Planarity : 0.004 0.048 4929 Dihedral : 5.308 103.829 3856 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.52 % Allowed : 11.83 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 3482 helix: 1.86 (0.13), residues: 1685 sheet: -0.40 (0.24), residues: 468 loop : -0.63 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2763 TYR 0.017 0.001 TYR A1546 PHE 0.013 0.001 PHE A1568 TRP 0.026 0.001 TRP B 261 HIS 0.004 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00368 (28528) covalent geometry : angle 0.55315 (38730) hydrogen bonds : bond 0.03687 ( 1513) hydrogen bonds : angle 4.27644 ( 4440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7357 (p0) cc_final: 0.6790 (t70) REVERT: A 1495 ASN cc_start: 0.8859 (m-40) cc_final: 0.8616 (m-40) REVERT: A 1564 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6676 (mp0) REVERT: A 1646 ASN cc_start: 0.8840 (t0) cc_final: 0.8502 (t0) REVERT: A 1649 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8403 (mttt) REVERT: A 1872 TYR cc_start: 0.8585 (t80) cc_final: 0.8265 (t80) REVERT: A 1958 ASP cc_start: 0.7107 (t70) cc_final: 0.6905 (t70) REVERT: A 1979 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: A 2018 MET cc_start: 0.8822 (mtm) cc_final: 0.8322 (mtm) REVERT: A 2239 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7536 (mptt) REVERT: A 2479 PHE cc_start: 0.8192 (m-80) cc_final: 0.7906 (m-80) REVERT: A 2555 ILE cc_start: 0.7517 (tp) cc_final: 0.7066 (pt) REVERT: A 2699 THR cc_start: 0.8669 (m) cc_final: 0.8084 (p) REVERT: A 2785 THR cc_start: 0.8525 (t) cc_final: 0.8232 (p) REVERT: A 2851 ASP cc_start: 0.8757 (m-30) cc_final: 0.8355 (m-30) REVERT: A 2888 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8340 (mt-10) REVERT: A 2987 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8578 (t0) REVERT: A 3077 ASP cc_start: 0.8065 (t70) cc_final: 0.7838 (t0) REVERT: A 3669 ILE cc_start: 0.7418 (mm) cc_final: 0.7184 (mm) REVERT: A 3676 VAL cc_start: 0.8937 (m) cc_final: 0.8722 (p) REVERT: A 3902 ASP cc_start: 0.8095 (m-30) cc_final: 0.7486 (t0) REVERT: A 4018 MET cc_start: 0.8846 (mtp) cc_final: 0.8393 (mtp) REVERT: A 4022 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7235 (mp0) REVERT: A 4092 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7586 (ptp-110) REVERT: A 4107 MET cc_start: 0.7562 (mmm) cc_final: 0.7331 (mmt) REVERT: A 4225 ASP cc_start: 0.8834 (t0) cc_final: 0.8592 (t70) REVERT: A 4295 GLN cc_start: 0.8658 (pt0) cc_final: 0.8260 (pm20) REVERT: B 201 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.5901 (ppp) REVERT: B 208 VAL cc_start: 0.9015 (m) cc_final: 0.8704 (m) REVERT: B 218 MET cc_start: 0.6982 (tpp) cc_final: 0.5603 (mpp) REVERT: B 219 TRP cc_start: 0.4190 (m-10) cc_final: 0.3432 (m100) REVERT: B 248 LEU cc_start: 0.7591 (tp) cc_final: 0.7288 (tt) REVERT: C 123 MET cc_start: 0.7476 (tmm) cc_final: 0.6835 (tmm) outliers start: 46 outliers final: 28 residues processed: 308 average time/residue: 0.1675 time to fit residues: 85.9551 Evaluate side-chains 293 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1979 GLN Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 2987 ASN Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3660 VAL Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4092 ARG Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4621 THR Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 268 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 347 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 297 optimal weight: 0.4980 chunk 282 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3854 GLN ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.135826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096107 restraints weight = 48574.624| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.05 r_work: 0.3209 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28528 Z= 0.107 Angle : 0.525 14.370 38730 Z= 0.262 Chirality : 0.041 0.267 4398 Planarity : 0.004 0.047 4929 Dihedral : 5.194 103.064 3856 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.49 % Allowed : 12.72 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.15), residues: 3482 helix: 1.96 (0.13), residues: 1692 sheet: -0.45 (0.24), residues: 473 loop : -0.59 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1467 TYR 0.016 0.001 TYR A1546 PHE 0.013 0.001 PHE A1568 TRP 0.024 0.001 TRP B 340 HIS 0.008 0.001 HIS A2560 Details of bonding type rmsd covalent geometry : bond 0.00239 (28528) covalent geometry : angle 0.52543 (38730) hydrogen bonds : bond 0.03389 ( 1513) hydrogen bonds : angle 4.12946 ( 4440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7332 (p0) cc_final: 0.6786 (t70) REVERT: A 1495 ASN cc_start: 0.8850 (m-40) cc_final: 0.8625 (m-40) REVERT: A 1564 GLU cc_start: 0.7709 (mm-30) cc_final: 0.6667 (mp0) REVERT: A 1646 ASN cc_start: 0.8821 (t0) cc_final: 0.8488 (t0) REVERT: A 1649 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8406 (mttt) REVERT: A 1872 TYR cc_start: 0.8573 (t80) cc_final: 0.8309 (t80) REVERT: A 1958 ASP cc_start: 0.7127 (t70) cc_final: 0.6903 (t70) REVERT: A 1967 MET cc_start: 0.8467 (tpp) cc_final: 0.7926 (mmm) REVERT: A 2018 MET cc_start: 0.8804 (mtm) cc_final: 0.8283 (mtm) REVERT: A 2239 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7620 (mptt) REVERT: A 2361 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8066 (mpp) REVERT: A 2479 PHE cc_start: 0.8199 (m-80) cc_final: 0.7900 (m-80) REVERT: A 2555 ILE cc_start: 0.7494 (tp) cc_final: 0.7027 (pt) REVERT: A 2699 THR cc_start: 0.8693 (m) cc_final: 0.8140 (p) REVERT: A 2785 THR cc_start: 0.8514 (t) cc_final: 0.8232 (p) REVERT: A 2836 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7758 (mtm-85) REVERT: A 2851 ASP cc_start: 0.8746 (m-30) cc_final: 0.8338 (m-30) REVERT: A 2888 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8366 (mt-10) REVERT: A 3077 ASP cc_start: 0.8056 (t70) cc_final: 0.7827 (t0) REVERT: A 3669 ILE cc_start: 0.7377 (mm) cc_final: 0.7160 (mm) REVERT: A 3676 VAL cc_start: 0.8918 (m) cc_final: 0.8715 (p) REVERT: A 3854 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7320 (pp30) REVERT: A 3902 ASP cc_start: 0.8075 (m-30) cc_final: 0.7441 (t0) REVERT: A 4018 MET cc_start: 0.8865 (mtp) cc_final: 0.8423 (mtp) REVERT: A 4022 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7239 (mp0) REVERT: A 4107 MET cc_start: 0.7476 (mmm) cc_final: 0.7240 (mmt) REVERT: A 4225 ASP cc_start: 0.8805 (t0) cc_final: 0.8567 (t70) REVERT: A 4295 GLN cc_start: 0.8588 (pt0) cc_final: 0.8201 (pm20) REVERT: B 201 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.5949 (ppp) REVERT: B 208 VAL cc_start: 0.8980 (m) cc_final: 0.8626 (m) REVERT: B 218 MET cc_start: 0.7072 (tpp) cc_final: 0.5842 (mpp) REVERT: B 219 TRP cc_start: 0.4081 (m-10) cc_final: 0.3487 (m100) REVERT: B 248 LEU cc_start: 0.7575 (tp) cc_final: 0.7283 (tt) REVERT: C 123 MET cc_start: 0.7438 (tmm) cc_final: 0.6736 (tmm) outliers start: 45 outliers final: 30 residues processed: 310 average time/residue: 0.1473 time to fit residues: 76.0273 Evaluate side-chains 303 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2485 GLN Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3854 GLN Chi-restraints excluded: chain A residue 3878 GLN Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 268 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 137 optimal weight: 4.9990 chunk 289 optimal weight: 30.0000 chunk 63 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 344 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 308 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2299 GLN ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2860 ASN A3069 ASN ** A3877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.130761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.091884 restraints weight = 48626.263| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.91 r_work: 0.3151 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28528 Z= 0.209 Angle : 0.598 14.299 38730 Z= 0.299 Chirality : 0.043 0.306 4398 Planarity : 0.004 0.047 4929 Dihedral : 5.350 105.258 3856 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.89 % Allowed : 13.75 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 3482 helix: 1.88 (0.13), residues: 1684 sheet: -0.46 (0.24), residues: 463 loop : -0.64 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3855 TYR 0.018 0.001 TYR A2792 PHE 0.016 0.002 PHE A2900 TRP 0.022 0.001 TRP B 340 HIS 0.008 0.001 HIS A3852 Details of bonding type rmsd covalent geometry : bond 0.00497 (28528) covalent geometry : angle 0.59815 (38730) hydrogen bonds : bond 0.03943 ( 1513) hydrogen bonds : angle 4.23696 ( 4440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 264 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7435 (p0) cc_final: 0.6860 (t70) REVERT: A 1495 ASN cc_start: 0.8798 (m-40) cc_final: 0.8534 (m-40) REVERT: A 1564 GLU cc_start: 0.7729 (mm-30) cc_final: 0.6664 (mp0) REVERT: A 1646 ASN cc_start: 0.8796 (t0) cc_final: 0.8477 (t0) REVERT: A 1649 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8477 (mttt) REVERT: A 1872 TYR cc_start: 0.8703 (t80) cc_final: 0.8329 (t80) REVERT: A 2018 MET cc_start: 0.8842 (mtm) cc_final: 0.8381 (mtm) REVERT: A 2239 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7641 (mptt) REVERT: A 2320 ASP cc_start: 0.7947 (t0) cc_final: 0.7491 (t0) REVERT: A 2361 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8107 (mpp) REVERT: A 2479 PHE cc_start: 0.8211 (m-80) cc_final: 0.7921 (m-80) REVERT: A 2555 ILE cc_start: 0.7511 (tp) cc_final: 0.7075 (pt) REVERT: A 2699 THR cc_start: 0.8759 (m) cc_final: 0.8233 (p) REVERT: A 2851 ASP cc_start: 0.8810 (m-30) cc_final: 0.8403 (m-30) REVERT: A 2888 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8399 (mt-10) REVERT: A 3077 ASP cc_start: 0.8116 (t70) cc_final: 0.7899 (t0) REVERT: A 3669 ILE cc_start: 0.7454 (mm) cc_final: 0.7212 (mm) REVERT: A 3825 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.5961 (p90) REVERT: A 3902 ASP cc_start: 0.8081 (m-30) cc_final: 0.7465 (t0) REVERT: A 4018 MET cc_start: 0.8890 (mtp) cc_final: 0.8463 (mtp) REVERT: A 4022 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7272 (mp0) REVERT: A 4107 MET cc_start: 0.7698 (mmm) cc_final: 0.7494 (mmt) REVERT: A 4225 ASP cc_start: 0.8897 (t0) cc_final: 0.8631 (t70) REVERT: A 4295 GLN cc_start: 0.8722 (pt0) cc_final: 0.8353 (pm20) REVERT: B 201 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.5872 (ppp) REVERT: B 208 VAL cc_start: 0.9071 (m) cc_final: 0.8744 (m) REVERT: B 218 MET cc_start: 0.7178 (tpp) cc_final: 0.5885 (mtp) REVERT: B 219 TRP cc_start: 0.4158 (m-10) cc_final: 0.3400 (m100) REVERT: B 248 LEU cc_start: 0.7601 (tp) cc_final: 0.7376 (tp) REVERT: C 123 MET cc_start: 0.7444 (tmm) cc_final: 0.6790 (tmm) outliers start: 57 outliers final: 40 residues processed: 299 average time/residue: 0.1471 time to fit residues: 73.8063 Evaluate side-chains 300 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2485 GLN Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2648 VAL Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3878 GLN Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4621 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 396 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 217 optimal weight: 0.7980 chunk 278 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 199 optimal weight: 0.0770 chunk 275 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3854 GLN A4381 HIS ** A4526 GLN ** 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 = 0.3878 r_free = 0.3878 target = 0.134093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.094310 restraints weight = 48480.591| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.03 r_work: 0.3183 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28528 Z= 0.124 Angle : 0.537 12.661 38730 Z= 0.269 Chirality : 0.041 0.315 4398 Planarity : 0.004 0.047 4929 Dihedral : 5.226 103.771 3856 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.59 % Allowed : 14.44 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.15), residues: 3482 helix: 1.96 (0.13), residues: 1692 sheet: -0.48 (0.24), residues: 464 loop : -0.58 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1467 TYR 0.016 0.001 TYR A1546 PHE 0.013 0.001 PHE A1568 TRP 0.020 0.001 TRP B 340 HIS 0.006 0.001 HIS A2560 Details of bonding type rmsd covalent geometry : bond 0.00284 (28528) covalent geometry : angle 0.53704 (38730) hydrogen bonds : bond 0.03522 ( 1513) hydrogen bonds : angle 4.08532 ( 4440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 271 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7374 (p0) cc_final: 0.6785 (t70) REVERT: A 1495 ASN cc_start: 0.8859 (m-40) cc_final: 0.8636 (m-40) REVERT: A 1564 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6751 (mp0) REVERT: A 1646 ASN cc_start: 0.8780 (t0) cc_final: 0.8449 (t0) REVERT: A 1649 LYS cc_start: 0.8681 (mmtp) cc_final: 0.8409 (mttt) REVERT: A 1872 TYR cc_start: 0.8600 (t80) cc_final: 0.8271 (t80) REVERT: A 1959 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7274 (mm-30) REVERT: A 2018 MET cc_start: 0.8871 (mtm) cc_final: 0.8362 (mtm) REVERT: A 2239 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7548 (mptt) REVERT: A 2320 ASP cc_start: 0.7914 (t0) cc_final: 0.7464 (t0) REVERT: A 2361 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8205 (mpp) REVERT: A 2461 MET cc_start: 0.8032 (mtp) cc_final: 0.7615 (mtp) REVERT: A 2555 ILE cc_start: 0.7478 (tp) cc_final: 0.7005 (pt) REVERT: A 2851 ASP cc_start: 0.8778 (m-30) cc_final: 0.8368 (m-30) REVERT: A 2888 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 3077 ASP cc_start: 0.8066 (t70) cc_final: 0.7849 (t0) REVERT: A 3669 ILE cc_start: 0.7368 (mm) cc_final: 0.7092 (mm) REVERT: A 3676 VAL cc_start: 0.8933 (m) cc_final: 0.8718 (p) REVERT: A 3825 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.5903 (p90) REVERT: A 3854 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7379 (pp30) REVERT: A 3902 ASP cc_start: 0.8054 (m-30) cc_final: 0.7404 (t0) REVERT: A 4022 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7230 (mp0) REVERT: A 4225 ASP cc_start: 0.8880 (t0) cc_final: 0.8622 (t70) REVERT: A 4295 GLN cc_start: 0.8616 (pt0) cc_final: 0.8224 (pm20) REVERT: B 201 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.5973 (ppp) REVERT: B 208 VAL cc_start: 0.9034 (m) cc_final: 0.8678 (m) REVERT: B 218 MET cc_start: 0.6966 (tpp) cc_final: 0.5821 (mtp) REVERT: B 219 TRP cc_start: 0.3845 (m-10) cc_final: 0.3134 (m100) REVERT: B 248 LEU cc_start: 0.7580 (tp) cc_final: 0.7351 (tp) REVERT: C 109 SER cc_start: 0.7551 (m) cc_final: 0.7322 (m) REVERT: C 123 MET cc_start: 0.7408 (tmm) cc_final: 0.6745 (tmm) outliers start: 48 outliers final: 32 residues processed: 298 average time/residue: 0.1541 time to fit residues: 75.7517 Evaluate side-chains 290 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1727 PHE Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3854 GLN Chi-restraints excluded: chain A residue 3878 GLN Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 348 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 274 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3854 GLN A3877 HIS ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.134123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.094368 restraints weight = 48675.237| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.02 r_work: 0.3186 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28528 Z= 0.127 Angle : 0.544 13.921 38730 Z= 0.270 Chirality : 0.041 0.335 4398 Planarity : 0.004 0.048 4929 Dihedral : 5.187 104.110 3856 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.69 % Allowed : 14.64 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.15), residues: 3482 helix: 2.01 (0.13), residues: 1691 sheet: -0.43 (0.24), residues: 464 loop : -0.57 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1467 TYR 0.016 0.001 TYR A1546 PHE 0.013 0.001 PHE A1568 TRP 0.018 0.001 TRP B 340 HIS 0.008 0.001 HIS A2560 Details of bonding type rmsd covalent geometry : bond 0.00294 (28528) covalent geometry : angle 0.54392 (38730) hydrogen bonds : bond 0.03480 ( 1513) hydrogen bonds : angle 4.05536 ( 4440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7380 (p0) cc_final: 0.6802 (t70) REVERT: A 1495 ASN cc_start: 0.8863 (m-40) cc_final: 0.8637 (m-40) REVERT: A 1564 GLU cc_start: 0.7754 (mm-30) cc_final: 0.6719 (mp0) REVERT: A 1646 ASN cc_start: 0.8779 (t0) cc_final: 0.8452 (t0) REVERT: A 1649 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8419 (mttt) REVERT: A 1872 TYR cc_start: 0.8605 (t80) cc_final: 0.8244 (t80) REVERT: A 1959 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7286 (mm-30) REVERT: A 2018 MET cc_start: 0.8869 (mtm) cc_final: 0.8367 (mtm) REVERT: A 2239 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7559 (mptt) REVERT: A 2320 ASP cc_start: 0.7921 (t0) cc_final: 0.7471 (t0) REVERT: A 2461 MET cc_start: 0.8075 (mtp) cc_final: 0.7668 (mtp) REVERT: A 2555 ILE cc_start: 0.7452 (tp) cc_final: 0.7010 (pt) REVERT: A 2851 ASP cc_start: 0.8764 (m-30) cc_final: 0.8354 (m-30) REVERT: A 2888 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8333 (mt-10) REVERT: A 2987 ASN cc_start: 0.8979 (t0) cc_final: 0.8612 (t0) REVERT: A 3076 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8367 (mtpt) REVERT: A 3077 ASP cc_start: 0.8059 (t70) cc_final: 0.7844 (t0) REVERT: A 3669 ILE cc_start: 0.7352 (mm) cc_final: 0.7070 (mm) REVERT: A 3825 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6078 (p90) REVERT: A 3854 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7366 (pp30) REVERT: A 3902 ASP cc_start: 0.8044 (m-30) cc_final: 0.7423 (t0) REVERT: A 4018 MET cc_start: 0.8774 (mtp) cc_final: 0.8164 (mtp) REVERT: A 4022 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7235 (mp0) REVERT: A 4225 ASP cc_start: 0.8875 (t0) cc_final: 0.8615 (t70) REVERT: A 4295 GLN cc_start: 0.8614 (pt0) cc_final: 0.8231 (pm20) REVERT: B 201 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.5953 (ppp) REVERT: B 208 VAL cc_start: 0.9064 (m) cc_final: 0.8674 (m) REVERT: B 218 MET cc_start: 0.7052 (tpp) cc_final: 0.5917 (mtt) REVERT: B 219 TRP cc_start: 0.3963 (m-10) cc_final: 0.3160 (m100) REVERT: B 248 LEU cc_start: 0.7542 (tp) cc_final: 0.7318 (tp) REVERT: C 123 MET cc_start: 0.7406 (tmm) cc_final: 0.6721 (tmm) outliers start: 51 outliers final: 39 residues processed: 296 average time/residue: 0.1522 time to fit residues: 74.6369 Evaluate side-chains 301 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1727 PHE Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3854 GLN Chi-restraints excluded: chain A residue 3878 GLN Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 3992 LEU Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 268 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 245 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 345 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 330 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3854 GLN ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.134752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095040 restraints weight = 48472.798| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.03 r_work: 0.3187 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28528 Z= 0.115 Angle : 0.534 13.734 38730 Z= 0.267 Chirality : 0.041 0.348 4398 Planarity : 0.004 0.047 4929 Dihedral : 5.138 103.827 3856 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.59 % Allowed : 14.91 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.15), residues: 3482 helix: 2.05 (0.13), residues: 1690 sheet: -0.42 (0.24), residues: 466 loop : -0.54 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1467 TYR 0.017 0.001 TYR A1546 PHE 0.013 0.001 PHE A2912 TRP 0.023 0.001 TRP C 365 HIS 0.008 0.001 HIS A2560 Details of bonding type rmsd covalent geometry : bond 0.00264 (28528) covalent geometry : angle 0.53396 (38730) hydrogen bonds : bond 0.03376 ( 1513) hydrogen bonds : angle 4.02191 ( 4440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7384 (p0) cc_final: 0.6816 (t70) REVERT: A 1495 ASN cc_start: 0.8865 (m-40) cc_final: 0.8645 (m-40) REVERT: A 1564 GLU cc_start: 0.7751 (mm-30) cc_final: 0.6731 (mp0) REVERT: A 1646 ASN cc_start: 0.8772 (t0) cc_final: 0.8451 (t0) REVERT: A 1649 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8410 (mttt) REVERT: A 1872 TYR cc_start: 0.8593 (t80) cc_final: 0.8251 (t80) REVERT: A 1959 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7235 (mm-30) REVERT: A 2018 MET cc_start: 0.8859 (mtm) cc_final: 0.8357 (mtm) REVERT: A 2239 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7598 (mptt) REVERT: A 2361 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8272 (mpp) REVERT: A 2481 MET cc_start: 0.6962 (tpt) cc_final: 0.6537 (mmm) REVERT: A 2555 ILE cc_start: 0.7480 (tp) cc_final: 0.7018 (pt) REVERT: A 2785 THR cc_start: 0.8546 (t) cc_final: 0.8261 (p) REVERT: A 2851 ASP cc_start: 0.8753 (m-30) cc_final: 0.8339 (m-30) REVERT: A 2888 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 2987 ASN cc_start: 0.8953 (t0) cc_final: 0.8609 (t0) REVERT: A 3076 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8365 (mtpt) REVERT: A 3077 ASP cc_start: 0.8068 (t70) cc_final: 0.7852 (t0) REVERT: A 3108 GLU cc_start: 0.8781 (tp30) cc_final: 0.8426 (tp30) REVERT: A 3669 ILE cc_start: 0.7326 (mm) cc_final: 0.7042 (mm) REVERT: A 3676 VAL cc_start: 0.8934 (m) cc_final: 0.8708 (p) REVERT: A 3825 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6037 (p90) REVERT: A 3854 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7551 (pp30) REVERT: A 3902 ASP cc_start: 0.8048 (m-30) cc_final: 0.7439 (t0) REVERT: A 4018 MET cc_start: 0.8782 (mtp) cc_final: 0.8283 (mtp) REVERT: A 4022 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7228 (mp0) REVERT: A 4225 ASP cc_start: 0.8848 (t0) cc_final: 0.8587 (t70) REVERT: A 4295 GLN cc_start: 0.8587 (pt0) cc_final: 0.8207 (pm20) REVERT: B 201 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.5964 (ppp) REVERT: B 208 VAL cc_start: 0.9032 (m) cc_final: 0.8629 (m) REVERT: B 218 MET cc_start: 0.7035 (tpp) cc_final: 0.5917 (mtt) REVERT: B 219 TRP cc_start: 0.4033 (m-10) cc_final: 0.3188 (m100) REVERT: B 248 LEU cc_start: 0.7535 (tp) cc_final: 0.7314 (tp) REVERT: C 109 SER cc_start: 0.7521 (m) cc_final: 0.7293 (m) REVERT: C 123 MET cc_start: 0.7418 (tmm) cc_final: 0.6724 (tmm) outliers start: 48 outliers final: 38 residues processed: 303 average time/residue: 0.1597 time to fit residues: 81.7523 Evaluate side-chains 305 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1727 PHE Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 2815 THR Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3854 GLN Chi-restraints excluded: chain A residue 3878 GLN Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 3992 LEU Chi-restraints excluded: chain A residue 4099 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 268 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 176 optimal weight: 8.9990 chunk 95 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3854 GLN ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** 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 = 0.3898 r_free = 0.3898 target = 0.135550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095908 restraints weight = 48416.178| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.05 r_work: 0.3212 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 28528 Z= 0.106 Angle : 0.539 13.758 38730 Z= 0.267 Chirality : 0.041 0.348 4398 Planarity : 0.004 0.049 4929 Dihedral : 5.083 103.828 3856 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.49 % Allowed : 15.44 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.15), residues: 3482 helix: 2.09 (0.13), residues: 1692 sheet: -0.42 (0.24), residues: 466 loop : -0.52 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3474 TYR 0.016 0.001 TYR A1546 PHE 0.013 0.001 PHE A2912 TRP 0.032 0.001 TRP B 340 HIS 0.008 0.001 HIS A2560 Details of bonding type rmsd covalent geometry : bond 0.00239 (28528) covalent geometry : angle 0.53863 (38730) hydrogen bonds : bond 0.03287 ( 1513) hydrogen bonds : angle 3.98834 ( 4440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.7367 (p0) cc_final: 0.6809 (t70) REVERT: A 1495 ASN cc_start: 0.8860 (m-40) cc_final: 0.8632 (m-40) REVERT: A 1564 GLU cc_start: 0.7787 (mm-30) cc_final: 0.6728 (mp0) REVERT: A 1646 ASN cc_start: 0.8763 (t0) cc_final: 0.8449 (t0) REVERT: A 1649 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8413 (mttt) REVERT: A 1872 TYR cc_start: 0.8596 (t80) cc_final: 0.8252 (t80) REVERT: A 1959 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 2018 MET cc_start: 0.8850 (mtm) cc_final: 0.8347 (mtm) REVERT: A 2239 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7593 (mptt) REVERT: A 2361 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8282 (mpp) REVERT: A 2481 MET cc_start: 0.6881 (tpt) cc_final: 0.6509 (mmm) REVERT: A 2555 ILE cc_start: 0.7478 (tp) cc_final: 0.7021 (pt) REVERT: A 2785 THR cc_start: 0.8557 (t) cc_final: 0.8277 (p) REVERT: A 2808 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 2851 ASP cc_start: 0.8753 (m-30) cc_final: 0.8327 (m-30) REVERT: A 2888 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 3076 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8338 (mtpt) REVERT: A 3077 ASP cc_start: 0.8064 (t70) cc_final: 0.7849 (t0) REVERT: A 3108 GLU cc_start: 0.8774 (tp30) cc_final: 0.8450 (tp30) REVERT: A 3676 VAL cc_start: 0.8942 (m) cc_final: 0.8721 (p) REVERT: A 3825 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.5978 (p90) REVERT: A 3854 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7446 (pp30) REVERT: A 3902 ASP cc_start: 0.8024 (m-30) cc_final: 0.7425 (t0) REVERT: A 4018 MET cc_start: 0.8777 (mtp) cc_final: 0.8195 (mtp) REVERT: A 4022 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7236 (mp0) REVERT: A 4225 ASP cc_start: 0.8841 (t0) cc_final: 0.8580 (t70) REVERT: A 4295 GLN cc_start: 0.8566 (pt0) cc_final: 0.8209 (pm20) REVERT: B 92 LYS cc_start: 0.5642 (mmtt) cc_final: 0.5043 (mppt) REVERT: B 201 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.5934 (ppp) REVERT: B 208 VAL cc_start: 0.9020 (m) cc_final: 0.8606 (m) REVERT: B 218 MET cc_start: 0.7038 (tpp) cc_final: 0.5926 (mtt) REVERT: B 219 TRP cc_start: 0.4005 (m-10) cc_final: 0.3159 (m100) REVERT: B 248 LEU cc_start: 0.7547 (tp) cc_final: 0.7330 (tp) REVERT: C 109 SER cc_start: 0.7542 (m) cc_final: 0.7318 (m) REVERT: C 123 MET cc_start: 0.7437 (tmm) cc_final: 0.6740 (tmm) outliers start: 45 outliers final: 33 residues processed: 300 average time/residue: 0.1617 time to fit residues: 80.5534 Evaluate side-chains 308 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1533 LEU Chi-restraints excluded: chain A residue 1676 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1727 PHE Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 2075 LEU Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2539 VAL Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2808 GLU Chi-restraints excluded: chain A residue 2813 LEU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3042 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3854 GLN Chi-restraints excluded: chain A residue 3878 GLN Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 268 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 229 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1985 HIS ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2987 ASN ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** 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 = 0.3897 r_free = 0.3897 target = 0.135419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.095745 restraints weight = 48483.154| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.05 r_work: 0.3210 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28528 Z= 0.111 Angle : 0.541 13.599 38730 Z= 0.268 Chirality : 0.041 0.338 4398 Planarity : 0.004 0.048 4929 Dihedral : 5.053 104.383 3856 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.42 % Allowed : 15.50 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.15), residues: 3482 helix: 2.13 (0.13), residues: 1686 sheet: -0.36 (0.24), residues: 462 loop : -0.51 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1467 TYR 0.017 0.001 TYR A1546 PHE 0.012 0.001 PHE A2912 TRP 0.043 0.001 TRP B 340 HIS 0.008 0.001 HIS A2560 Details of bonding type rmsd covalent geometry : bond 0.00252 (28528) covalent geometry : angle 0.54119 (38730) hydrogen bonds : bond 0.03265 ( 1513) hydrogen bonds : angle 3.96921 ( 4440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6561.70 seconds wall clock time: 113 minutes 13.69 seconds (6793.69 seconds total)