Starting phenix.real_space_refine on Fri Sep 19 09:44:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0w_47372/09_2025/9e0w_47372.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0w_47372/09_2025/9e0w_47372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e0w_47372/09_2025/9e0w_47372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0w_47372/09_2025/9e0w_47372.map" model { file = "/net/cci-nas-00/data/ceres_data/9e0w_47372/09_2025/9e0w_47372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0w_47372/09_2025/9e0w_47372.cif" } resolution = 3.2 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 128 5.16 5 C 15596 2.51 5 N 4255 2.21 5 O 4541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24531 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 21923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2782, 21923 Classifications: {'peptide': 2782} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PCIS': 3, 'PTRANS': 125, 'TRANS': 2653} Chain breaks: 12 Unresolved non-hydrogen bonds: 431 Unresolved non-hydrogen angles: 538 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 26, 'ASP:plan': 13, 'ASN:plan1': 5, 'TYR:plan': 5, 'ARG:plan': 10, 'GLN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 306 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: 5.93, per 1000 atoms: 0.24 Number of scatterers: 24531 At special positions: 0 Unit cell: (113.135, 147.73, 200.09, 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 128 16.00 P 9 15.00 Mg 2 11.99 O 4541 8.00 N 4255 7.00 C 15596 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: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5894 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 26 sheets defined 55.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 1556 through 1561 removed outlier: 3.734A pdb=" N LEU A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.945A 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 1617 through 1626 removed outlier: 4.325A pdb=" N ARG A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A1625 " --> pdb=" O ARG A1621 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 removed outlier: 3.737A pdb=" N TYR A1630 " --> pdb=" O PRO A1627 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A1632 " --> pdb=" O PHE A1629 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1627 through 1632' Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 3.671A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.842A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1768 Processing helix chain 'A' and resid 1776 through 1797 Processing helix chain 'A' and resid 1801 through 1828 removed outlier: 3.680A pdb=" N SER A1828 " --> pdb=" O SER A1824 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 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 1986 removed outlier: 3.773A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 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: 3.757A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2114 removed outlier: 3.872A 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 2152 through 2165 removed outlier: 4.277A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2231 through 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2311 through 2316 removed outlier: 3.774A pdb=" N ASN A2316 " --> pdb=" O GLU A2313 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2370 through 2384 removed outlier: 3.549A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2424 Processing helix chain 'A' and resid 2425 through 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2432 through 2443 removed outlier: 3.545A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.731A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.666A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) removed outlier: 4.105A 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 2548 through 2552 Processing helix chain 'A' and resid 2571 through 2586 Processing helix chain 'A' and resid 2600 through 2610 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 2740 through 2756 removed outlier: 4.940A pdb=" N GLN A2746 " --> pdb=" O ALA A2742 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 3.773A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2782 Processing helix chain 'A' and resid 2795 through 2810 removed outlier: 3.847A 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 2902 removed outlier: 4.254A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.937A 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 removed outlier: 3.645A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) 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: 3.918A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.644A 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 3073 through 3082 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 Processing helix chain 'A' and resid 3172 through 3240 removed outlier: 3.720A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3451 through 3500 removed outlier: 4.256A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A3488 " --> pdb=" O ALA A3484 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A3491 " --> pdb=" O GLU A3487 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.584A 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 3548 through 3554 removed outlier: 3.827A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.678A 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 3637 through 3641 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 4.013A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A3696 " --> pdb=" O LEU A3692 " (cutoff:3.500A) 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: 3.542A pdb=" N ASP A3762 " --> pdb=" O ARG A3759 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A3763 " --> pdb=" O ILE A3760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3759 through 3763' Processing helix chain 'A' and resid 3764 through 3818 removed outlier: 4.108A pdb=" N VAL A3784 " --> pdb=" O VAL A3780 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU A3785 " --> pdb=" O THR A3781 " (cutoff:3.500A) removed outlier: 4.078A 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: 3.748A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.917A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 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: 3.952A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.703A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.793A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 4.907A 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: 3.633A 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: 3.732A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.765A 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 4317 through 4322 Processing helix chain 'A' and resid 4328 through 4349 removed outlier: 3.916A pdb=" N LEU A4349 " --> pdb=" O LYS A4345 " (cutoff:3.500A) 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 4497 removed outlier: 3.674A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) Processing helix chain 'A' and resid 4512 through 4514 No H-bonds generated for 'chain 'A' and resid 4512 through 4514' Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.769A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4539 removed outlier: 3.897A pdb=" N LEU A4539 " --> pdb=" O LEU A4536 " (cutoff:3.500A) Processing helix chain 'A' and resid 4631 through 4638 Processing helix chain 'C' and resid 90 through 94 removed outlier: 4.031A pdb=" N TRP C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 297 removed outlier: 3.639A pdb=" N TYR C 290 " --> pdb=" O PRO C 286 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER C 292 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1663 through 1665 removed outlier: 10.713A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA3, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1928 removed outlier: 6.919A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR A2017 " --> pdb=" O GLY A1955 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE A1957 " --> pdb=" O THR A2017 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA6, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 6.925A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA8, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AA9, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.289A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 3.870A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.501A pdb=" N SER A2874 " --> pdb=" O ILE A2882 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.517A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.143A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 5.946A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 6.892A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N CYS A4286 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LYS A4292 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4508 through 4510 removed outlier: 6.205A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4564 through 4566 removed outlier: 3.754A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AC2, first strand: chain 'C' and resid 95 through 96 removed outlier: 5.660A pdb=" N THR C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER C 399 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS C 405 " --> pdb=" O THR C 397 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 397 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 396 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C 387 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER C 385 " --> pdb=" O GLY C 398 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.656A pdb=" N ALA C 126 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL C 114 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL C 124 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 134 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG C 144 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 156 through 158 removed outlier: 4.366A pdb=" N ARG C 186 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASP C 178 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS C 184 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 197 through 200 removed outlier: 3.775A pdb=" N MET C 218 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS C 228 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU C 220 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N CYS C 226 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 239 through 242 removed outlier: 3.818A pdb=" N MET C 239 " --> pdb=" O CYS C 252 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 258 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU C 271 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL C 260 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 279 through 284 removed outlier: 3.916A pdb=" N SER C 315 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET C 322 " --> pdb=" O MET C 332 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET C 332 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP C 324 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N CYS C 330 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 341 through 346 removed outlier: 3.990A pdb=" N GLY C 343 " --> pdb=" O CYS C 356 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C 362 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR C 375 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL C 364 " --> pdb=" O MET C 373 " (cutoff:3.500A) 1358 hydrogen bonds defined for protein. 3975 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: 7.83 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8062 1.34 - 1.46: 5433 1.46 - 1.58: 11336 1.58 - 1.70: 13 1.70 - 1.82: 210 Bond restraints: 25054 Sorted by residual: bond pdb=" CA THR A3900 " pdb=" CB THR A3900 " ideal model delta sigma weight residual 1.532 1.557 -0.025 1.36e-02 5.41e+03 3.43e+00 bond pdb=" CD2 TYR A2873 " pdb=" CE2 TYR A2873 " ideal model delta sigma weight residual 1.382 1.335 0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CA MET A2189 " pdb=" C MET A2189 " ideal model delta sigma weight residual 1.524 1.546 -0.022 1.48e-02 4.57e+03 2.17e+00 bond pdb=" CB GLU A3776 " pdb=" CG GLU A3776 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CE2 TYR A2873 " pdb=" CZ TYR A2873 " ideal model delta sigma weight residual 1.378 1.344 0.034 2.40e-02 1.74e+03 2.03e+00 ... (remaining 25049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 33351 1.87 - 3.75: 537 3.75 - 5.62: 96 5.62 - 7.49: 29 7.49 - 9.37: 5 Bond angle restraints: 34018 Sorted by residual: angle pdb=" N LEU A2668 " pdb=" CA LEU A2668 " pdb=" C LEU A2668 " ideal model delta sigma weight residual 109.81 118.29 -8.48 2.21e+00 2.05e-01 1.47e+01 angle pdb=" CA MET A2189 " pdb=" CB MET A2189 " pdb=" CG MET A2189 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA THR A3900 " pdb=" CB THR A3900 " pdb=" CG2 THR A3900 " ideal model delta sigma weight residual 110.50 116.96 -6.46 1.70e+00 3.46e-01 1.44e+01 angle pdb=" C GLU A1694 " pdb=" N HIS A1695 " pdb=" CA HIS A1695 " ideal model delta sigma weight residual 122.83 126.85 -4.02 1.08e+00 8.57e-01 1.39e+01 angle pdb=" C PRO A2870 " pdb=" N ILE A2871 " pdb=" CA ILE A2871 " ideal model delta sigma weight residual 121.97 127.76 -5.79 1.80e+00 3.09e-01 1.03e+01 ... (remaining 34013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 13863 21.36 - 42.72: 1118 42.72 - 64.07: 118 64.07 - 85.43: 32 85.43 - 106.79: 5 Dihedral angle restraints: 15136 sinusoidal: 6085 harmonic: 9051 Sorted by residual: dihedral pdb=" O1B ADP A4805 " pdb=" O3A ADP A4805 " pdb=" PB ADP A4805 " pdb=" PA ADP A4805 " ideal model delta sinusoidal sigma weight residual -60.00 46.79 -106.79 1 2.00e+01 2.50e-03 3.09e+01 dihedral pdb=" CA GLU A3776 " pdb=" C GLU A3776 " pdb=" N ALA A3777 " pdb=" CA ALA A3777 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA GLU A1964 " pdb=" C GLU A1964 " pdb=" N GLU A1965 " pdb=" CA GLU A1965 " ideal model delta harmonic sigma weight residual 180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 15133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2956 0.046 - 0.092: 720 0.092 - 0.138: 189 0.138 - 0.184: 11 0.184 - 0.230: 4 Chirality restraints: 3880 Sorted by residual: chirality pdb=" CA GLU A3776 " pdb=" N GLU A3776 " pdb=" C GLU A3776 " pdb=" CB GLU A3776 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+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 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB THR A3900 " pdb=" CA THR A3900 " pdb=" OG1 THR A3900 " pdb=" CG2 THR A3900 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3877 not shown) Planarity restraints: 4339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1727 " -0.015 2.00e-02 2.50e+03 1.89e-02 6.25e+00 pdb=" CG PHE A1727 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A1727 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A1727 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A1727 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1727 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1727 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A4391 " -0.039 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A4392 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A4392 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A4392 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A3149 " -0.013 2.00e-02 2.50e+03 1.54e-02 4.15e+00 pdb=" CG PHE A3149 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A3149 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A3149 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A3149 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A3149 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A3149 " 0.000 2.00e-02 2.50e+03 ... (remaining 4336 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 173 2.55 - 3.14: 18088 3.14 - 3.72: 39551 3.72 - 4.31: 51186 4.31 - 4.90: 87880 Nonbonded interactions: 196878 Sorted by model distance: nonbonded pdb=" O1G ATP A4802 " pdb="MG MG A4803 " model vdw 1.962 2.170 nonbonded pdb=" O2B ATP A4802 " pdb="MG MG A4803 " model vdw 1.992 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4803 " model vdw 2.010 2.170 nonbonded pdb=" O2B ADP A4801 " pdb="MG MG A4806 " model vdw 2.019 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4803 " model vdw 2.100 2.170 ... (remaining 196873 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.220 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 0.047 25054 Z= 0.142 Angle : 0.611 9.368 34018 Z= 0.308 Chirality : 0.043 0.230 3880 Planarity : 0.004 0.058 4339 Dihedral : 15.034 106.791 9242 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.04 % Allowed : 2.08 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 0.62 (0.15), residues: 3065 helix: 1.32 (0.13), residues: 1574 sheet: 0.55 (0.30), residues: 338 loop : -0.85 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2863 TYR 0.016 0.001 TYR A2496 PHE 0.044 0.001 PHE A1727 TRP 0.016 0.001 TRP A1701 HIS 0.011 0.001 HIS A2827 Details of bonding type rmsd covalent geometry : bond 0.00311 (25054) covalent geometry : angle 0.61076 (34018) hydrogen bonds : bond 0.10613 ( 1356) hydrogen bonds : angle 5.30215 ( 3975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 1.215 Fit side-chains REVERT: A 1943 ARG cc_start: 0.8458 (tpt-90) cc_final: 0.8056 (tpt-90) REVERT: A 2112 LYS cc_start: 0.6752 (mptt) cc_final: 0.6010 (mtpt) REVERT: A 2801 ARG cc_start: 0.7897 (mmm160) cc_final: 0.7648 (mtp-110) REVERT: A 2996 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 3169 MET cc_start: 0.8152 (mmt) cc_final: 0.7822 (mmt) REVERT: A 3591 ASP cc_start: 0.8259 (t70) cc_final: 0.7608 (p0) REVERT: A 3885 MET cc_start: 0.8072 (tpp) cc_final: 0.7856 (tpp) REVERT: A 4433 ASP cc_start: 0.9028 (m-30) cc_final: 0.8776 (m-30) REVERT: A 4571 ASN cc_start: 0.8800 (m-40) cc_final: 0.8352 (p0) REVERT: C 113 ARG cc_start: 0.6128 (mmm160) cc_final: 0.5771 (mmt-90) REVERT: C 116 PHE cc_start: 0.3492 (m-80) cc_final: 0.3000 (m-80) REVERT: C 123 MET cc_start: 0.7212 (mmt) cc_final: 0.5867 (tmm) REVERT: C 182 PHE cc_start: 0.4405 (m-10) cc_final: 0.3967 (m-10) REVERT: C 249 ILE cc_start: 0.6863 (pt) cc_final: 0.6517 (mt) REVERT: C 310 PHE cc_start: 0.2909 (m-10) cc_final: 0.1167 (m-80) REVERT: C 373 MET cc_start: 0.7681 (ptm) cc_final: 0.7343 (ptt) REVERT: C 384 THR cc_start: 0.4145 (p) cc_final: 0.3604 (p) outliers start: 1 outliers final: 1 residues processed: 272 average time/residue: 0.1680 time to fit residues: 74.4105 Evaluate side-chains 210 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2471 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN C 254 ASN C 337 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.137205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.100952 restraints weight = 46488.962| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.08 r_work: 0.3309 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25054 Z= 0.161 Angle : 0.553 8.437 34018 Z= 0.276 Chirality : 0.041 0.163 3880 Planarity : 0.004 0.054 4339 Dihedral : 5.774 105.763 3405 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.94 % Allowed : 8.01 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.06 (0.15), residues: 3065 helix: 1.74 (0.13), residues: 1594 sheet: 0.45 (0.30), residues: 331 loop : -0.69 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3870 TYR 0.013 0.001 TYR A2748 PHE 0.016 0.001 PHE A3149 TRP 0.015 0.001 TRP A1701 HIS 0.010 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00377 (25054) covalent geometry : angle 0.55311 (34018) hydrogen bonds : bond 0.03629 ( 1356) hydrogen bonds : angle 4.36321 ( 3975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 2112 LYS cc_start: 0.6738 (mptt) cc_final: 0.5958 (mtpt) REVERT: A 2481 MET cc_start: 0.7971 (tpt) cc_final: 0.7515 (tpt) REVERT: A 2615 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8395 (mtt) REVERT: A 2636 ASP cc_start: 0.8550 (t0) cc_final: 0.8343 (t0) REVERT: A 2801 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7746 (mtp-110) REVERT: A 2998 ASN cc_start: 0.8245 (m110) cc_final: 0.8021 (m110) REVERT: A 3169 MET cc_start: 0.8117 (mmt) cc_final: 0.7800 (mmt) REVERT: A 3591 ASP cc_start: 0.8495 (t70) cc_final: 0.7882 (p0) REVERT: A 3667 GLN cc_start: 0.6479 (tt0) cc_final: 0.5998 (pm20) REVERT: A 3826 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7341 (mt0) REVERT: A 4332 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 4433 ASP cc_start: 0.9110 (m-30) cc_final: 0.8844 (m-30) REVERT: A 4571 ASN cc_start: 0.8840 (m-40) cc_final: 0.8297 (p0) REVERT: C 113 ARG cc_start: 0.6060 (mmm160) cc_final: 0.5554 (mmt180) REVERT: C 115 ILE cc_start: 0.1499 (pt) cc_final: 0.1092 (pt) REVERT: C 116 PHE cc_start: 0.3345 (m-80) cc_final: 0.2903 (m-80) REVERT: C 123 MET cc_start: 0.7640 (mmt) cc_final: 0.6108 (tmm) REVERT: C 182 PHE cc_start: 0.4593 (m-10) cc_final: 0.4150 (m-10) REVERT: C 249 ILE cc_start: 0.6511 (pt) cc_final: 0.6016 (mt) REVERT: C 371 ARG cc_start: 0.5035 (ttp80) cc_final: 0.4664 (ttp-170) REVERT: C 373 MET cc_start: 0.7642 (ptm) cc_final: 0.7411 (ptt) REVERT: C 384 THR cc_start: 0.4067 (p) cc_final: 0.3473 (p) outliers start: 25 outliers final: 16 residues processed: 245 average time/residue: 0.1773 time to fit residues: 70.0674 Evaluate side-chains 233 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1631 PHE Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3826 GLN Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4332 LEU Chi-restraints excluded: chain C residue 216 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 150 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.137513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100997 restraints weight = 46479.352| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.80 r_work: 0.3326 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25054 Z= 0.134 Angle : 0.525 8.176 34018 Z= 0.261 Chirality : 0.040 0.164 3880 Planarity : 0.004 0.055 4339 Dihedral : 5.689 105.121 3405 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.36 % Allowed : 10.42 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.20 (0.16), residues: 3065 helix: 1.89 (0.13), residues: 1594 sheet: 0.31 (0.29), residues: 334 loop : -0.62 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2285 TYR 0.024 0.001 TYR A3836 PHE 0.011 0.001 PHE A3179 TRP 0.015 0.001 TRP A1701 HIS 0.006 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00312 (25054) covalent geometry : angle 0.52502 (34018) hydrogen bonds : bond 0.03481 ( 1356) hydrogen bonds : angle 4.14114 ( 3975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.029 Fit side-chains REVERT: A 2112 LYS cc_start: 0.6755 (mptt) cc_final: 0.5993 (mtpt) REVERT: A 2481 MET cc_start: 0.8012 (tpt) cc_final: 0.7645 (tpt) REVERT: A 2615 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8378 (mtt) REVERT: A 2801 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7763 (mtp-110) REVERT: A 2998 ASN cc_start: 0.8264 (m110) cc_final: 0.8036 (m110) REVERT: A 3108 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 3169 MET cc_start: 0.8111 (mmt) cc_final: 0.7796 (mmt) REVERT: A 3591 ASP cc_start: 0.8582 (t70) cc_final: 0.7865 (p0) REVERT: A 3667 GLN cc_start: 0.6502 (tt0) cc_final: 0.5975 (pm20) REVERT: A 4095 MET cc_start: 0.9007 (ttt) cc_final: 0.8666 (ttt) REVERT: A 4433 ASP cc_start: 0.9103 (m-30) cc_final: 0.8843 (m-30) REVERT: A 4516 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8095 (m) REVERT: A 4571 ASN cc_start: 0.8862 (m-40) cc_final: 0.8318 (p0) REVERT: C 113 ARG cc_start: 0.6285 (mmm160) cc_final: 0.5737 (mmt180) REVERT: C 115 ILE cc_start: 0.1593 (pt) cc_final: 0.1285 (pt) REVERT: C 116 PHE cc_start: 0.3703 (m-80) cc_final: 0.3145 (m-80) REVERT: C 123 MET cc_start: 0.7764 (mmt) cc_final: 0.6125 (tmm) REVERT: C 182 PHE cc_start: 0.4408 (m-10) cc_final: 0.3972 (m-10) REVERT: C 220 GLU cc_start: 0.5791 (mm-30) cc_final: 0.5352 (mm-30) REVERT: C 249 ILE cc_start: 0.6656 (pt) cc_final: 0.6080 (mt) REVERT: C 259 ARG cc_start: 0.5403 (mtt180) cc_final: 0.5190 (mtp180) REVERT: C 371 ARG cc_start: 0.5171 (ttp80) cc_final: 0.4749 (ttp-170) REVERT: C 384 THR cc_start: 0.4345 (p) cc_final: 0.3799 (p) outliers start: 36 outliers final: 26 residues processed: 242 average time/residue: 0.1680 time to fit residues: 65.4693 Evaluate side-chains 241 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3826 GLN Chi-restraints excluded: chain A residue 3885 MET Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 297 optimal weight: 50.0000 chunk 113 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 121 optimal weight: 0.0980 chunk 4 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN C 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.138216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.101707 restraints weight = 46282.358| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.81 r_work: 0.3339 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25054 Z= 0.111 Angle : 0.503 7.825 34018 Z= 0.248 Chirality : 0.039 0.161 3880 Planarity : 0.003 0.053 4339 Dihedral : 5.604 104.314 3405 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.57 % Rotamer: Outliers : 1.59 % Allowed : 12.01 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.34 (0.16), residues: 3065 helix: 2.02 (0.13), residues: 1594 sheet: 0.33 (0.29), residues: 333 loop : -0.55 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2285 TYR 0.015 0.001 TYR A3836 PHE 0.010 0.001 PHE A2343 TRP 0.014 0.001 TRP A1701 HIS 0.006 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00252 (25054) covalent geometry : angle 0.50257 (34018) hydrogen bonds : bond 0.03257 ( 1356) hydrogen bonds : angle 3.98596 ( 3975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.786 Fit side-chains REVERT: A 2112 LYS cc_start: 0.6842 (mptt) cc_final: 0.6104 (mtpt) REVERT: A 2615 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8373 (mtt) REVERT: A 2801 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7762 (mtp-110) REVERT: A 2998 ASN cc_start: 0.8228 (m110) cc_final: 0.8000 (m110) REVERT: A 3169 MET cc_start: 0.8104 (mmt) cc_final: 0.7790 (mmt) REVERT: A 3591 ASP cc_start: 0.8572 (t70) cc_final: 0.7866 (p0) REVERT: A 3667 GLN cc_start: 0.6400 (tt0) cc_final: 0.5884 (pm20) REVERT: A 3836 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: A 4095 MET cc_start: 0.9013 (ttt) cc_final: 0.8696 (ttt) REVERT: A 4108 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7333 (pt0) REVERT: A 4433 ASP cc_start: 0.9087 (m-30) cc_final: 0.8826 (m-30) REVERT: A 4571 ASN cc_start: 0.8864 (m-40) cc_final: 0.8312 (p0) REVERT: C 113 ARG cc_start: 0.6251 (mmm160) cc_final: 0.5744 (mmt180) REVERT: C 115 ILE cc_start: 0.1584 (pt) cc_final: 0.1206 (pt) REVERT: C 116 PHE cc_start: 0.3525 (m-80) cc_final: 0.3107 (m-80) REVERT: C 123 MET cc_start: 0.7711 (mmt) cc_final: 0.6044 (tmm) REVERT: C 182 PHE cc_start: 0.4435 (m-10) cc_final: 0.4007 (m-10) REVERT: C 220 GLU cc_start: 0.5850 (mm-30) cc_final: 0.5388 (mm-30) REVERT: C 249 ILE cc_start: 0.6698 (pt) cc_final: 0.6128 (mt) REVERT: C 259 ARG cc_start: 0.5478 (mtt180) cc_final: 0.5208 (mtp85) REVERT: C 371 ARG cc_start: 0.5130 (ttp80) cc_final: 0.4768 (ttp-170) REVERT: C 373 MET cc_start: 0.7632 (ptm) cc_final: 0.7432 (ptt) REVERT: C 384 THR cc_start: 0.4423 (p) cc_final: 0.3812 (p) outliers start: 42 outliers final: 27 residues processed: 245 average time/residue: 0.1634 time to fit residues: 64.3134 Evaluate side-chains 246 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3178 ASP Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3826 GLN Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 265 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 142 optimal weight: 0.0870 chunk 111 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 221 optimal weight: 0.0070 chunk 68 optimal weight: 0.0470 chunk 66 optimal weight: 0.8980 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.137927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.101293 restraints weight = 46186.524| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.82 r_work: 0.3333 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25054 Z= 0.116 Angle : 0.504 8.927 34018 Z= 0.248 Chirality : 0.039 0.166 3880 Planarity : 0.003 0.055 4339 Dihedral : 5.567 105.072 3405 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 2.04 % Allowed : 12.76 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.42 (0.16), residues: 3065 helix: 2.08 (0.13), residues: 1594 sheet: 0.45 (0.30), residues: 325 loop : -0.53 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3695 TYR 0.016 0.001 TYR A3836 PHE 0.021 0.001 PHE A4410 TRP 0.015 0.001 TRP A1701 HIS 0.017 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00268 (25054) covalent geometry : angle 0.50361 (34018) hydrogen bonds : bond 0.03244 ( 1356) hydrogen bonds : angle 3.92597 ( 3975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 1.041 Fit side-chains REVERT: A 2112 LYS cc_start: 0.6805 (mptt) cc_final: 0.6066 (mtpt) REVERT: A 2332 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.6784 (mtp85) REVERT: A 2615 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: A 2801 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7759 (mtp-110) REVERT: A 2998 ASN cc_start: 0.8259 (m110) cc_final: 0.8029 (m110) REVERT: A 3169 MET cc_start: 0.8096 (mmt) cc_final: 0.7790 (mmt) REVERT: A 3591 ASP cc_start: 0.8582 (t70) cc_final: 0.7875 (p0) REVERT: A 3667 GLN cc_start: 0.6350 (tt0) cc_final: 0.5893 (pm20) REVERT: A 3836 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6153 (m-80) REVERT: A 3927 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 4095 MET cc_start: 0.9045 (ttt) cc_final: 0.8732 (ttt) REVERT: A 4108 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: A 4433 ASP cc_start: 0.9097 (m-30) cc_final: 0.8835 (m-30) REVERT: A 4516 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8045 (m) REVERT: A 4571 ASN cc_start: 0.8875 (m-40) cc_final: 0.8308 (p0) REVERT: C 113 ARG cc_start: 0.6315 (mmm160) cc_final: 0.5789 (mmt180) REVERT: C 115 ILE cc_start: 0.1678 (pt) cc_final: 0.1311 (pt) REVERT: C 116 PHE cc_start: 0.3274 (m-80) cc_final: 0.2899 (m-80) REVERT: C 123 MET cc_start: 0.7638 (mmt) cc_final: 0.5906 (tmm) REVERT: C 182 PHE cc_start: 0.4474 (m-10) cc_final: 0.4072 (m-10) REVERT: C 220 GLU cc_start: 0.5871 (mm-30) cc_final: 0.5358 (mm-30) REVERT: C 249 ILE cc_start: 0.6662 (pt) cc_final: 0.6073 (mt) REVERT: C 259 ARG cc_start: 0.5328 (mtt180) cc_final: 0.5092 (mtp85) REVERT: C 321 LYS cc_start: 0.5739 (mmtm) cc_final: 0.5188 (mmtm) REVERT: C 323 TRP cc_start: 0.4208 (OUTLIER) cc_final: 0.3892 (m100) REVERT: C 341 VAL cc_start: 0.8595 (t) cc_final: 0.8173 (t) REVERT: C 371 ARG cc_start: 0.5192 (ttp80) cc_final: 0.4857 (ttp-170) REVERT: C 373 MET cc_start: 0.7622 (ptm) cc_final: 0.7382 (ptt) REVERT: C 384 THR cc_start: 0.4511 (p) cc_final: 0.3869 (p) outliers start: 54 outliers final: 38 residues processed: 246 average time/residue: 0.1670 time to fit residues: 65.7392 Evaluate side-chains 257 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3826 GLN Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3885 MET Chi-restraints excluded: chain A residue 3927 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4332 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 181 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 136 optimal weight: 0.0070 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2746 GLN ** C 206 HIS ** 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 = 0.3988 r_free = 0.3988 target = 0.136059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100513 restraints weight = 46304.737| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.06 r_work: 0.3277 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25054 Z= 0.152 Angle : 0.532 9.942 34018 Z= 0.263 Chirality : 0.040 0.167 3880 Planarity : 0.004 0.056 4339 Dihedral : 5.631 107.354 3405 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 2.19 % Allowed : 13.56 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.37 (0.16), residues: 3065 helix: 2.04 (0.13), residues: 1597 sheet: 0.32 (0.29), residues: 345 loop : -0.55 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2285 TYR 0.020 0.001 TYR A3836 PHE 0.014 0.001 PHE A3179 TRP 0.014 0.001 TRP A1701 HIS 0.006 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00362 (25054) covalent geometry : angle 0.53233 (34018) hydrogen bonds : bond 0.03479 ( 1356) hydrogen bonds : angle 3.95476 ( 3975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 0.994 Fit side-chains REVERT: A 1615 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6349 (pp) REVERT: A 2112 LYS cc_start: 0.6848 (mptt) cc_final: 0.6093 (mtpt) REVERT: A 2320 ASP cc_start: 0.8040 (t0) cc_final: 0.7839 (t0) REVERT: A 2332 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.6726 (mtp85) REVERT: A 2615 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8381 (mtt) REVERT: A 2801 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7807 (mtp-110) REVERT: A 2998 ASN cc_start: 0.8339 (m110) cc_final: 0.8095 (m110) REVERT: A 3044 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7156 (mm) REVERT: A 3169 MET cc_start: 0.8204 (mmt) cc_final: 0.7882 (mmt) REVERT: A 3591 ASP cc_start: 0.8574 (t70) cc_final: 0.7829 (p0) REVERT: A 3667 GLN cc_start: 0.6391 (tt0) cc_final: 0.5872 (pm20) REVERT: A 3836 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: A 3927 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8261 (pp) REVERT: A 4095 MET cc_start: 0.9177 (ttt) cc_final: 0.8881 (ttt) REVERT: A 4108 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: A 4233 ILE cc_start: 0.8986 (mt) cc_final: 0.8659 (tt) REVERT: A 4433 ASP cc_start: 0.9160 (m-30) cc_final: 0.8909 (m-30) REVERT: A 4516 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7993 (m) REVERT: A 4571 ASN cc_start: 0.8887 (m-40) cc_final: 0.8269 (p0) REVERT: C 113 ARG cc_start: 0.6228 (mmm160) cc_final: 0.5717 (mmt180) REVERT: C 116 PHE cc_start: 0.3078 (m-80) cc_final: 0.2686 (m-80) REVERT: C 123 MET cc_start: 0.7601 (mmt) cc_final: 0.5771 (tmm) REVERT: C 182 PHE cc_start: 0.4385 (m-10) cc_final: 0.3981 (m-10) REVERT: C 220 GLU cc_start: 0.5889 (mm-30) cc_final: 0.5428 (mm-30) REVERT: C 249 ILE cc_start: 0.6752 (pt) cc_final: 0.6176 (mt) REVERT: C 259 ARG cc_start: 0.5324 (mtt180) cc_final: 0.5108 (mtp180) REVERT: C 321 LYS cc_start: 0.5544 (mmtm) cc_final: 0.4945 (mmtm) REVERT: C 371 ARG cc_start: 0.5069 (ttp80) cc_final: 0.4705 (ttp-170) REVERT: C 373 MET cc_start: 0.7570 (ptm) cc_final: 0.7334 (ptt) REVERT: C 384 THR cc_start: 0.4499 (p) cc_final: 0.3841 (p) outliers start: 58 outliers final: 39 residues processed: 244 average time/residue: 0.1736 time to fit residues: 68.1751 Evaluate side-chains 248 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2746 GLN Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 2990 ILE Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3826 GLN Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3885 MET Chi-restraints excluded: chain A residue 3927 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 17 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 92 optimal weight: 0.0170 chunk 182 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 233 optimal weight: 0.5980 chunk 299 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN A1779 HIS ** C 206 HIS ** 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 = 0.4014 r_free = 0.4014 target = 0.138125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102523 restraints weight = 45973.415| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.25 r_work: 0.3319 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.002 0.038 25054 Z= 0.099 Angle : 0.502 8.790 34018 Z= 0.247 Chirality : 0.039 0.164 3880 Planarity : 0.003 0.056 4339 Dihedral : 5.526 105.647 3405 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 1.89 % Allowed : 14.46 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.53 (0.16), residues: 3065 helix: 2.19 (0.13), residues: 1591 sheet: 0.43 (0.29), residues: 349 loop : -0.52 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2285 TYR 0.016 0.001 TYR A3836 PHE 0.023 0.001 PHE A4410 TRP 0.017 0.001 TRP C 323 HIS 0.005 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00217 (25054) covalent geometry : angle 0.50182 (34018) hydrogen bonds : bond 0.03169 ( 1356) hydrogen bonds : angle 3.83653 ( 3975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 0.901 Fit side-chains REVERT: A 2041 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7610 (ptp) REVERT: A 2112 LYS cc_start: 0.6932 (mptt) cc_final: 0.6236 (mtpt) REVERT: A 2332 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.6685 (mtp85) REVERT: A 2615 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8417 (mtt) REVERT: A 2801 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7804 (mtp-110) REVERT: A 2998 ASN cc_start: 0.8343 (m110) cc_final: 0.8098 (m110) REVERT: A 3169 MET cc_start: 0.8128 (mmt) cc_final: 0.7819 (mmt) REVERT: A 3591 ASP cc_start: 0.8522 (t70) cc_final: 0.7802 (p0) REVERT: A 3667 GLN cc_start: 0.6377 (tt0) cc_final: 0.5881 (pm20) REVERT: A 3836 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: A 3927 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8247 (pp) REVERT: A 4095 MET cc_start: 0.9112 (ttt) cc_final: 0.8860 (ttt) REVERT: A 4233 ILE cc_start: 0.8975 (mt) cc_final: 0.8659 (tt) REVERT: A 4252 TYR cc_start: 0.8800 (m-80) cc_final: 0.8432 (m-80) REVERT: A 4433 ASP cc_start: 0.9097 (m-30) cc_final: 0.8838 (m-30) REVERT: A 4516 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8006 (m) REVERT: A 4571 ASN cc_start: 0.8882 (m-40) cc_final: 0.8258 (p0) REVERT: C 113 ARG cc_start: 0.6227 (mmm160) cc_final: 0.5726 (mmt180) REVERT: C 122 VAL cc_start: 0.4965 (t) cc_final: 0.4512 (t) REVERT: C 123 MET cc_start: 0.7568 (mmt) cc_final: 0.5758 (ttp) REVERT: C 182 PHE cc_start: 0.4352 (m-10) cc_final: 0.3975 (m-10) REVERT: C 220 GLU cc_start: 0.5996 (mm-30) cc_final: 0.5454 (mm-30) REVERT: C 249 ILE cc_start: 0.6611 (pt) cc_final: 0.6017 (mt) REVERT: C 371 ARG cc_start: 0.5147 (ttp80) cc_final: 0.4789 (ttp-170) REVERT: C 373 MET cc_start: 0.7686 (ptm) cc_final: 0.7440 (ptt) REVERT: C 384 THR cc_start: 0.4488 (p) cc_final: 0.3835 (p) outliers start: 50 outliers final: 32 residues processed: 242 average time/residue: 0.1709 time to fit residues: 66.2049 Evaluate side-chains 240 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3885 MET Chi-restraints excluded: chain A residue 3927 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 115 optimal weight: 0.5980 chunk 213 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 188 optimal weight: 0.1980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2746 GLN ** C 206 HIS ** 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 = 0.3973 r_free = 0.3973 target = 0.134852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099075 restraints weight = 46302.665| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.08 r_work: 0.3259 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25054 Z= 0.185 Angle : 0.567 10.567 34018 Z= 0.280 Chirality : 0.041 0.165 3880 Planarity : 0.004 0.058 4339 Dihedral : 5.687 108.733 3405 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 2.27 % Allowed : 14.43 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.38 (0.16), residues: 3065 helix: 2.05 (0.13), residues: 1597 sheet: 0.25 (0.29), residues: 355 loop : -0.50 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 259 TYR 0.022 0.001 TYR A3836 PHE 0.017 0.001 PHE A3179 TRP 0.014 0.001 TRP A1701 HIS 0.006 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00444 (25054) covalent geometry : angle 0.56734 (34018) hydrogen bonds : bond 0.03644 ( 1356) hydrogen bonds : angle 3.97688 ( 3975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 1.012 Fit side-chains REVERT: A 1615 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6392 (pp) REVERT: A 2112 LYS cc_start: 0.6993 (mptt) cc_final: 0.6240 (mtpt) REVERT: A 2191 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 2332 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.6642 (mtp85) REVERT: A 2615 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8367 (mtt) REVERT: A 2801 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7817 (mtp-110) REVERT: A 2998 ASN cc_start: 0.8337 (m110) cc_final: 0.8096 (m110) REVERT: A 3044 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7209 (mm) REVERT: A 3169 MET cc_start: 0.8225 (mmt) cc_final: 0.7890 (mmt) REVERT: A 3667 GLN cc_start: 0.6510 (tt0) cc_final: 0.5985 (pm20) REVERT: A 3836 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.6307 (m-80) REVERT: A 3885 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7890 (ttp) REVERT: A 3927 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8303 (pp) REVERT: A 4095 MET cc_start: 0.9226 (ttt) cc_final: 0.8953 (ttt) REVERT: A 4107 MET cc_start: 0.7548 (mmt) cc_final: 0.7293 (mmt) REVERT: A 4233 ILE cc_start: 0.8998 (mt) cc_final: 0.8709 (tt) REVERT: A 4252 TYR cc_start: 0.8910 (m-80) cc_final: 0.8594 (m-80) REVERT: A 4571 ASN cc_start: 0.8886 (m-40) cc_final: 0.8274 (p0) REVERT: C 107 HIS cc_start: 0.4014 (OUTLIER) cc_final: 0.3705 (t-90) REVERT: C 113 ARG cc_start: 0.6181 (mmm160) cc_final: 0.5744 (mmt180) REVERT: C 122 VAL cc_start: 0.5032 (t) cc_final: 0.4569 (t) REVERT: C 123 MET cc_start: 0.7596 (mmt) cc_final: 0.5691 (ttp) REVERT: C 182 PHE cc_start: 0.4342 (m-10) cc_final: 0.3990 (m-10) REVERT: C 249 ILE cc_start: 0.6846 (pt) cc_final: 0.6248 (mt) REVERT: C 371 ARG cc_start: 0.5064 (ttp80) cc_final: 0.4662 (ttp-170) REVERT: C 373 MET cc_start: 0.7661 (ptm) cc_final: 0.7424 (ptt) REVERT: C 384 THR cc_start: 0.4446 (p) cc_final: 0.3762 (p) outliers start: 60 outliers final: 41 residues processed: 237 average time/residue: 0.1744 time to fit residues: 67.1294 Evaluate side-chains 244 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2599 SER Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3885 MET Chi-restraints excluded: chain A residue 3927 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 224 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 284 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 300 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3542 GLN A3735 GLN ** C 206 HIS ** 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 = 0.3982 r_free = 0.3982 target = 0.135545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100216 restraints weight = 46363.923| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.08 r_work: 0.3266 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25054 Z= 0.148 Angle : 0.544 10.174 34018 Z= 0.268 Chirality : 0.040 0.159 3880 Planarity : 0.004 0.057 4339 Dihedral : 5.675 107.260 3405 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 2.15 % Allowed : 14.88 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.42 (0.16), residues: 3065 helix: 2.08 (0.13), residues: 1596 sheet: 0.21 (0.29), residues: 355 loop : -0.47 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2285 TYR 0.018 0.001 TYR A3836 PHE 0.018 0.001 PHE A4482 TRP 0.016 0.001 TRP A1701 HIS 0.005 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00352 (25054) covalent geometry : angle 0.54396 (34018) hydrogen bonds : bond 0.03501 ( 1356) hydrogen bonds : angle 3.93234 ( 3975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 1.074 Fit side-chains REVERT: A 2112 LYS cc_start: 0.6996 (mptt) cc_final: 0.6318 (mtpt) REVERT: A 2191 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8142 (mm) REVERT: A 2332 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.6652 (mtp85) REVERT: A 2615 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8376 (mtt) REVERT: A 2801 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7802 (mtp-110) REVERT: A 2996 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 3044 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7125 (mm) REVERT: A 3169 MET cc_start: 0.8244 (mmt) cc_final: 0.7858 (mmt) REVERT: A 3206 ARG cc_start: 0.7221 (ttp-110) cc_final: 0.6890 (ttp-170) REVERT: A 3516 TYR cc_start: 0.8432 (m-80) cc_final: 0.7668 (m-80) REVERT: A 3667 GLN cc_start: 0.6391 (tt0) cc_final: 0.5852 (pm20) REVERT: A 3836 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: A 3927 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8276 (pp) REVERT: A 4095 MET cc_start: 0.9187 (ttt) cc_final: 0.8961 (ttt) REVERT: A 4107 MET cc_start: 0.7534 (mmt) cc_final: 0.7276 (mmt) REVERT: A 4128 MET cc_start: 0.8532 (ptp) cc_final: 0.8324 (ptp) REVERT: A 4233 ILE cc_start: 0.8981 (mt) cc_final: 0.8700 (tt) REVERT: A 4252 TYR cc_start: 0.8837 (m-80) cc_final: 0.8557 (m-80) REVERT: A 4571 ASN cc_start: 0.8876 (m-40) cc_final: 0.8278 (p0) REVERT: C 107 HIS cc_start: 0.4103 (OUTLIER) cc_final: 0.3842 (t-90) REVERT: C 113 ARG cc_start: 0.6025 (mmm160) cc_final: 0.5634 (mmt180) REVERT: C 122 VAL cc_start: 0.5248 (t) cc_final: 0.4808 (t) REVERT: C 123 MET cc_start: 0.7606 (mmt) cc_final: 0.5734 (ttp) REVERT: C 182 PHE cc_start: 0.4522 (m-10) cc_final: 0.4209 (m-10) REVERT: C 220 GLU cc_start: 0.5548 (mm-30) cc_final: 0.4464 (mp0) REVERT: C 371 ARG cc_start: 0.4884 (ttp80) cc_final: 0.4472 (ttp-170) REVERT: C 373 MET cc_start: 0.7617 (ptm) cc_final: 0.7399 (ptt) REVERT: C 384 THR cc_start: 0.4279 (p) cc_final: 0.3586 (p) outliers start: 57 outliers final: 45 residues processed: 233 average time/residue: 0.1710 time to fit residues: 64.6432 Evaluate side-chains 247 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1631 PHE Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2599 SER Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3885 MET Chi-restraints excluded: chain A residue 3927 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 180 optimal weight: 3.9990 chunk 284 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 198 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN ** A2079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** 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 = 0.3891 r_free = 0.3891 target = 0.132631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096097 restraints weight = 45382.025| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.82 r_work: 0.3184 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25054 Z= 0.151 Angle : 0.554 10.318 34018 Z= 0.273 Chirality : 0.040 0.160 3880 Planarity : 0.004 0.058 4339 Dihedral : 5.689 107.391 3405 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 2.11 % Allowed : 14.92 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.38 (0.16), residues: 3065 helix: 2.06 (0.13), residues: 1602 sheet: 0.19 (0.29), residues: 355 loop : -0.52 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3870 TYR 0.019 0.001 TYR A3836 PHE 0.014 0.001 PHE A3179 TRP 0.015 0.001 TRP A1701 HIS 0.006 0.001 HIS A4389 Details of bonding type rmsd covalent geometry : bond 0.00361 (25054) covalent geometry : angle 0.55375 (34018) hydrogen bonds : bond 0.03537 ( 1356) hydrogen bonds : angle 3.94534 ( 3975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 0.849 Fit side-chains REVERT: A 2112 LYS cc_start: 0.7008 (mptt) cc_final: 0.6328 (mtpt) REVERT: A 2191 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8117 (mm) REVERT: A 2332 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.6551 (mtp85) REVERT: A 2615 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8431 (mtt) REVERT: A 2632 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8391 (mt) REVERT: A 2995 ASP cc_start: 0.7440 (t0) cc_final: 0.7134 (t70) REVERT: A 2996 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7432 (tm-30) REVERT: A 3044 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6982 (mm) REVERT: A 3169 MET cc_start: 0.8062 (mmt) cc_final: 0.7738 (mmt) REVERT: A 3206 ARG cc_start: 0.7155 (ttp-110) cc_final: 0.6760 (ttp-170) REVERT: A 3516 TYR cc_start: 0.8463 (m-80) cc_final: 0.7838 (m-80) REVERT: A 3667 GLN cc_start: 0.6345 (tt0) cc_final: 0.5750 (pm20) REVERT: A 3836 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6408 (m-80) REVERT: A 3885 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7848 (ttp) REVERT: A 3927 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8245 (pp) REVERT: A 4095 MET cc_start: 0.9283 (ttt) cc_final: 0.9063 (ttt) REVERT: A 4107 MET cc_start: 0.7466 (mmt) cc_final: 0.7208 (mmt) REVERT: A 4128 MET cc_start: 0.8488 (ptp) cc_final: 0.8213 (ptp) REVERT: A 4233 ILE cc_start: 0.8950 (mt) cc_final: 0.8667 (tt) REVERT: A 4252 TYR cc_start: 0.8822 (m-80) cc_final: 0.8455 (m-80) REVERT: A 4482 PHE cc_start: 0.8251 (t80) cc_final: 0.7913 (t80) REVERT: A 4571 ASN cc_start: 0.8883 (m-40) cc_final: 0.8189 (p0) REVERT: C 107 HIS cc_start: 0.4418 (OUTLIER) cc_final: 0.4082 (t-90) REVERT: C 113 ARG cc_start: 0.6212 (mmm160) cc_final: 0.5737 (mmt180) REVERT: C 122 VAL cc_start: 0.5077 (t) cc_final: 0.4633 (t) REVERT: C 123 MET cc_start: 0.7564 (mmt) cc_final: 0.5642 (ttp) REVERT: C 182 PHE cc_start: 0.4327 (m-10) cc_final: 0.4039 (m-10) REVERT: C 220 GLU cc_start: 0.5517 (mm-30) cc_final: 0.4263 (mp0) REVERT: C 371 ARG cc_start: 0.5117 (ttp80) cc_final: 0.4667 (ttp-170) REVERT: C 373 MET cc_start: 0.7694 (ptm) cc_final: 0.7441 (ptt) REVERT: C 384 THR cc_start: 0.4481 (p) cc_final: 0.3795 (p) outliers start: 56 outliers final: 44 residues processed: 235 average time/residue: 0.1703 time to fit residues: 64.4043 Evaluate side-chains 250 residues out of total 2753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1631 PHE Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2202 MET Chi-restraints excluded: chain A residue 2205 GLU Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2345 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2355 THR Chi-restraints excluded: chain A residue 2423 MET Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2599 SER Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2632 LEU Chi-restraints excluded: chain A residue 2686 MET Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2779 MET Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3044 LEU Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3740 LEU Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3885 MET Chi-restraints excluded: chain A residue 3927 LEU Chi-restraints excluded: chain A residue 4007 MET Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4114 HIS Chi-restraints excluded: chain A residue 4317 THR Chi-restraints excluded: chain A residue 4388 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 143 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 279 optimal weight: 0.3980 chunk 116 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** A2560 HIS A2998 ASN ** C 206 HIS ** 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 = 0.3895 r_free = 0.3895 target = 0.132943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096459 restraints weight = 45134.851| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.81 r_work: 0.3190 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25054 Z= 0.140 Angle : 0.549 10.772 34018 Z= 0.270 Chirality : 0.040 0.159 3880 Planarity : 0.003 0.057 4339 Dihedral : 5.671 106.989 3405 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 2.11 % Allowed : 15.14 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.44 (0.16), residues: 3065 helix: 2.10 (0.13), residues: 1596 sheet: 0.21 (0.29), residues: 355 loop : -0.47 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2285 TYR 0.018 0.001 TYR A3836 PHE 0.012 0.001 PHE A3179 TRP 0.015 0.001 TRP A1701 HIS 0.012 0.001 HIS A2560 Details of bonding type rmsd covalent geometry : bond 0.00333 (25054) covalent geometry : angle 0.54865 (34018) hydrogen bonds : bond 0.03482 ( 1356) hydrogen bonds : angle 3.91901 ( 3975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6357.45 seconds wall clock time: 109 minutes 44.40 seconds (6584.40 seconds total)