Starting phenix.real_space_refine on Fri Sep 19 05:13:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0k_47360/09_2025/9e0k_47360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0k_47360/09_2025/9e0k_47360.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 { model { file = "/net/cci-nas-00/data/ceres_data/9e0k_47360/09_2025/9e0k_47360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0k_47360/09_2025/9e0k_47360.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e0k_47360/09_2025/9e0k_47360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0k_47360/09_2025/9e0k_47360.map" } 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= 0.030 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 111 5.16 5 C 14608 2.51 5 N 3964 2.21 5 O 4236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s 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: 22930 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2892, 22816 Classifications: {'peptide': 2892} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PCIS': 4, 'PTRANS': 125, 'TRANS': 2762} Chain breaks: 13 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 30, 'ASP:plan': 13, 'ASN:plan1': 5, 'TYR:plan': 5, 'ARG:plan': 10, 'HIS:plan': 3, 'PHE:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 330 Chain: "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: 5.64, per 1000 atoms: 0.25 Number of scatterers: 22930 At special positions: 0 Unit cell: (112.2, 138.38, 208.505, 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 111 16.00 P 9 15.00 Mg 2 11.99 O 4236 8.00 N 3964 7.00 C 14608 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: 2.06 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5516 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 22 sheets defined 62.3% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 1444 through 1472 Processing helix chain 'A' and resid 1490 through 1510 removed outlier: 3.513A pdb=" N SER A1510 " --> pdb=" O ALA A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1515 removed outlier: 3.607A pdb=" N VAL A1515 " --> pdb=" O TYR A1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1512 through 1515' Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.808A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.735A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1594 removed outlier: 3.731A pdb=" N ILE A1594 " --> pdb=" O ASP A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1615 Processing helix chain 'A' and resid 1616 through 1624 removed outlier: 4.170A pdb=" N GLU A1620 " --> pdb=" O GLY A1616 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1632 removed outlier: 3.519A pdb=" N TYR A1630 " --> pdb=" O PRO A1627 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1644 through 1646 No H-bonds generated for 'chain 'A' and resid 1644 through 1646' Processing helix chain 'A' and resid 1647 through 1651 removed outlier: 4.033A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.647A pdb=" N ARG A1710 " --> pdb=" O GLU A1706 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A1729 " --> pdb=" O GLU A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1768 removed outlier: 3.707A pdb=" N SER A1768 " --> pdb=" O THR A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1797 Processing helix chain 'A' and resid 1801 through 1828 removed outlier: 3.739A 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 1987 removed outlier: 3.833A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.009A 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: 3.677A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2114 removed outlier: 3.821A pdb=" N GLU A2114 " --> pdb=" O LYS A2110 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2311 through 2314 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2370 through 2384 removed outlier: 3.728A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2428 Proline residue: A2425 - end of helix removed outlier: 3.730A pdb=" N THR A2428 " --> pdb=" O GLN A2424 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2443 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.857A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 4.056A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2571 through 2586 Processing helix chain 'A' and resid 2600 through 2610 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.386A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2739 through 2756 removed outlier: 4.054A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A2746 " --> pdb=" O ALA A2742 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 3.709A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 4.533A pdb=" N ARG A2783 " --> pdb=" O MET A2779 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A2784 " --> pdb=" O SER A2780 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.832A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.536A pdb=" N LEU A2889 " --> pdb=" O ASP A2885 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.764A pdb=" N GLN A2928 " --> pdb=" O ARG A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 4.141A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 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: 3.551A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3451 through 3502 removed outlier: 4.877A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN A3498 " --> pdb=" O GLU A3494 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3517 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 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 removed outlier: 3.646A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 3.843A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) removed outlier: 3.691A 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 Processing helix chain 'A' and resid 3764 through 3818 removed outlier: 4.292A pdb=" N VAL A3784 " --> pdb=" O VAL A3780 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU A3785 " --> pdb=" O THR A3781 " (cutoff:3.500A) removed outlier: 4.321A 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 3842 removed outlier: 3.611A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A3841 " --> pdb=" O HIS A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.774A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3894 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3928 through 3940 removed outlier: 4.020A pdb=" N CYS A3940 " --> pdb=" O VAL A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 removed outlier: 3.772A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4026 through 4035 removed outlier: 3.772A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A4035 " --> pdb=" O VAL A4031 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 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: 4.651A 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: 3.614A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4193 removed outlier: 4.361A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.635A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.833A 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 4324 through 4327 Processing helix chain 'A' and resid 4328 through 4350 removed outlier: 4.399A pdb=" N LEU A4349 " --> pdb=" O LYS A4345 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU A4350 " --> pdb=" O MET A4346 " (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 4498 removed outlier: 4.111A 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 Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.812A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 10.511A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.522A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 removed outlier: 3.559A pdb=" N ALA A1864 " --> pdb=" O MET A1861 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1928 removed outlier: 7.025A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR A2017 " --> pdb=" O GLY A1955 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A1957 " --> pdb=" O THR A2017 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 6.958A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A2345 " --> pdb=" O MET A2222 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.495A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 4.221A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A2699 " --> pdb=" O ARG A2694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.710A pdb=" N SER A2874 " --> pdb=" O ILE A2882 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2958 through 2959 removed outlier: 6.389A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3587 through 3590 Processing sheet with id=AB7, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.076A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3654 through 3656 removed outlier: 3.781A pdb=" N LEU A3661 " --> pdb=" O ARG A3654 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 3.617A pdb=" N THR A4067 " --> pdb=" O TRP A4093 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 6.936A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N CYS A4286 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LYS A4292 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.405A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 4564 through 4565 removed outlier: 6.241A pdb=" N VAL A4605 " --> pdb=" O ASP A4623 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP A4623 " --> pdb=" O VAL A4605 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A4607 " --> pdb=" O THR A4621 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR A4621 " --> pdb=" O LEU A4607 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A4609 " --> pdb=" O ILE A4619 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 4568 through 4571 1376 hydrogen bonds defined for protein. 4035 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: 6.83 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7512 1.34 - 1.46: 3644 1.46 - 1.58: 12055 1.58 - 1.69: 12 1.69 - 1.81: 185 Bond restraints: 23408 Sorted by residual: bond pdb=" C ILE A4391 " pdb=" N PRO A4392 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.86e+00 bond pdb=" CA PHE A3823 " pdb=" CB PHE A3823 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.67e+00 bond pdb=" CD1 TYR A3836 " pdb=" CE1 TYR A3836 " ideal model delta sigma weight residual 1.382 1.345 0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" CA ILE A2385 " pdb=" CB ILE A2385 " ideal model delta sigma weight residual 1.537 1.552 -0.015 1.29e-02 6.01e+03 1.33e+00 bond pdb=" CA GLU A2814 " pdb=" CB GLU A2814 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.27e+00 ... (remaining 23403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 31177 2.00 - 3.99: 503 3.99 - 5.99: 79 5.99 - 7.98: 21 7.98 - 9.98: 10 Bond angle restraints: 31790 Sorted by residual: angle pdb=" N LEU A2668 " pdb=" CA LEU A2668 " pdb=" C LEU A2668 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 angle pdb=" C ALA A1862 " pdb=" N ASN A1863 " pdb=" CA ASN A1863 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" CB ARG A4159 " pdb=" CG ARG A4159 " pdb=" CD ARG A4159 " ideal model delta sigma weight residual 111.30 120.44 -9.14 2.30e+00 1.89e-01 1.58e+01 angle pdb=" C LEU A2813 " pdb=" N GLU A2814 " pdb=" CA GLU A2814 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C SER A2384 " pdb=" N ILE A2385 " pdb=" CA ILE A2385 " ideal model delta sigma weight residual 122.13 127.69 -5.56 1.85e+00 2.92e-01 9.03e+00 ... (remaining 31785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.30: 13426 27.30 - 54.60: 660 54.60 - 81.90: 62 81.90 - 109.20: 9 109.20 - 136.50: 1 Dihedral angle restraints: 14158 sinusoidal: 5688 harmonic: 8470 Sorted by residual: dihedral pdb=" O2A ADP A4806 " pdb=" O3A ADP A4806 " pdb=" PA ADP A4806 " pdb=" PB ADP A4806 " ideal model delta sinusoidal sigma weight residual -60.00 76.50 -136.50 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" CA LEU A2813 " pdb=" C LEU A2813 " pdb=" N GLU A2814 " pdb=" CA GLU A2814 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.48e+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 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 14155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2726 0.045 - 0.090: 695 0.090 - 0.135: 195 0.135 - 0.179: 16 0.179 - 0.224: 6 Chirality restraints: 3638 Sorted by residual: chirality pdb=" CB ILE A3924 " pdb=" CA ILE A3924 " pdb=" CG1 ILE A3924 " pdb=" CG2 ILE A3924 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU A3745 " pdb=" CB LEU A3745 " pdb=" CD1 LEU A3745 " pdb=" CD2 LEU A3745 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE A2385 " pdb=" CA ILE A2385 " pdb=" CG1 ILE A2385 " pdb=" CG2 ILE A2385 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 3635 not shown) Planarity restraints: 4057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A4148 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A4149 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A4149 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A4149 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1510 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A1511 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1511 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1511 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2795 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A2796 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A2796 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2796 " 0.027 5.00e-02 4.00e+02 ... (remaining 4054 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 146 2.55 - 3.14: 17101 3.14 - 3.73: 37156 3.73 - 4.31: 47424 4.31 - 4.90: 81783 Nonbonded interactions: 183610 Sorted by model distance: nonbonded pdb=" O2B ATP A4803 " pdb="MG MG A4804 " model vdw 1.964 2.170 nonbonded pdb=" O1G ATP A4803 " pdb="MG MG A4804 " model vdw 1.985 2.170 nonbonded pdb=" O2B ADP A4801 " pdb="MG MG A4802 " model vdw 2.024 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4804 " model vdw 2.075 2.170 nonbonded pdb=" OD2 ASP A1958 " pdb="MG MG A4802 " model vdw 2.142 2.170 ... (remaining 183605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 0.038 23408 Z= 0.151 Angle : 0.644 9.979 31790 Z= 0.318 Chirality : 0.043 0.224 3638 Planarity : 0.005 0.052 4057 Dihedral : 15.096 136.501 8642 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.04 % Allowed : 1.75 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.72 (0.15), residues: 2864 helix: 1.33 (0.12), residues: 1668 sheet: -0.25 (0.35), residues: 238 loop : -0.79 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A4159 TYR 0.019 0.001 TYR A2638 PHE 0.020 0.001 PHE A1926 TRP 0.018 0.001 TRP A2845 HIS 0.005 0.001 HIS A3175 Details of bonding type rmsd covalent geometry : bond 0.00337 (23408) covalent geometry : angle 0.64411 (31790) hydrogen bonds : bond 0.09807 ( 1376) hydrogen bonds : angle 5.02797 ( 4035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.939 Fit side-chains REVERT: A 1490 TRP cc_start: 0.7803 (m100) cc_final: 0.7591 (m100) REVERT: A 1491 ASP cc_start: 0.8458 (p0) cc_final: 0.7932 (t0) REVERT: A 1507 MET cc_start: 0.7786 (tmm) cc_final: 0.7508 (tmm) REVERT: A 1523 TRP cc_start: 0.7337 (m100) cc_final: 0.6586 (m100) REVERT: A 1533 LEU cc_start: 0.8713 (mm) cc_final: 0.7831 (tt) REVERT: A 1580 LYS cc_start: 0.7631 (ttpt) cc_final: 0.7120 (mptt) REVERT: A 1621 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8098 (tpm170) REVERT: A 1877 ASP cc_start: 0.8303 (m-30) cc_final: 0.8031 (m-30) REVERT: A 2074 LYS cc_start: 0.8563 (tptt) cc_final: 0.8125 (ttpt) REVERT: A 2163 ASP cc_start: 0.8722 (t0) cc_final: 0.8202 (m-30) REVERT: A 2187 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 2446 ILE cc_start: 0.9084 (tp) cc_final: 0.8822 (tp) REVERT: A 2874 SER cc_start: 0.9006 (t) cc_final: 0.8573 (p) REVERT: A 3077 ASP cc_start: 0.8633 (t0) cc_final: 0.8273 (m-30) REVERT: A 3188 HIS cc_start: 0.7793 (t70) cc_final: 0.7593 (t70) REVERT: A 3506 ASP cc_start: 0.8597 (t0) cc_final: 0.8171 (t0) REVERT: A 3534 HIS cc_start: 0.8344 (t-170) cc_final: 0.8077 (t-170) REVERT: A 3683 ASP cc_start: 0.8477 (t0) cc_final: 0.8098 (t0) REVERT: A 4425 GLN cc_start: 0.8754 (pt0) cc_final: 0.8323 (tp40) outliers start: 1 outliers final: 0 residues processed: 296 average time/residue: 0.1483 time to fit residues: 71.0351 Evaluate side-chains 226 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1855 GLN ** A1863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1922 GLN A4488 GLN A4530 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101819 restraints weight = 42402.021| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.68 r_work: 0.3269 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23408 Z= 0.116 Angle : 0.536 8.207 31790 Z= 0.264 Chirality : 0.039 0.153 3638 Planarity : 0.004 0.049 4057 Dihedral : 5.799 133.030 3188 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.69 % Allowed : 8.09 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.30 (0.16), residues: 2864 helix: 1.84 (0.13), residues: 1684 sheet: -0.32 (0.35), residues: 227 loop : -0.55 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4159 TYR 0.014 0.001 TYR A1546 PHE 0.032 0.001 PHE A3149 TRP 0.017 0.001 TRP A4387 HIS 0.008 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00256 (23408) covalent geometry : angle 0.53560 (31790) hydrogen bonds : bond 0.03444 ( 1376) hydrogen bonds : angle 4.03213 ( 4035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.991 Fit side-chains REVERT: A 1490 TRP cc_start: 0.7759 (m100) cc_final: 0.7535 (m100) REVERT: A 1491 ASP cc_start: 0.8494 (p0) cc_final: 0.8014 (t0) REVERT: A 1507 MET cc_start: 0.7645 (tmm) cc_final: 0.7310 (tmm) REVERT: A 1523 TRP cc_start: 0.7295 (m100) cc_final: 0.6586 (m100) REVERT: A 1533 LEU cc_start: 0.8719 (mm) cc_final: 0.7825 (tt) REVERT: A 1580 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7185 (mptt) REVERT: A 1621 ARG cc_start: 0.8525 (mtp85) cc_final: 0.8023 (tpm170) REVERT: A 1877 ASP cc_start: 0.8317 (m-30) cc_final: 0.8052 (m-30) REVERT: A 2074 LYS cc_start: 0.8541 (tptt) cc_final: 0.8103 (ttpt) REVERT: A 2163 ASP cc_start: 0.8700 (t0) cc_final: 0.8275 (m-30) REVERT: A 2187 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 2446 ILE cc_start: 0.9080 (tp) cc_final: 0.8819 (tp) REVERT: A 2874 SER cc_start: 0.8948 (t) cc_final: 0.8391 (p) REVERT: A 3077 ASP cc_start: 0.8603 (t0) cc_final: 0.8284 (m-30) REVERT: A 3500 MET cc_start: 0.9062 (mmm) cc_final: 0.8141 (tpp) REVERT: A 3506 ASP cc_start: 0.8601 (t0) cc_final: 0.8195 (t0) REVERT: A 3534 HIS cc_start: 0.8256 (t-170) cc_final: 0.8049 (t-170) REVERT: A 3683 ASP cc_start: 0.8452 (t0) cc_final: 0.8121 (t0) REVERT: A 3815 MET cc_start: 0.8482 (ttt) cc_final: 0.8159 (ttt) REVERT: A 3862 ASP cc_start: 0.8500 (m-30) cc_final: 0.8158 (t0) REVERT: A 4425 GLN cc_start: 0.8780 (pt0) cc_final: 0.8291 (tp40) outliers start: 17 outliers final: 9 residues processed: 265 average time/residue: 0.1553 time to fit residues: 67.1434 Evaluate side-chains 230 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 221 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 268 optimal weight: 0.7980 chunk 258 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 255 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1876 GLN ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3200 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102230 restraints weight = 42350.978| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.68 r_work: 0.3275 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23408 Z= 0.109 Angle : 0.517 7.850 31790 Z= 0.254 Chirality : 0.038 0.150 3638 Planarity : 0.004 0.053 4057 Dihedral : 5.679 132.664 3188 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.77 % Allowed : 10.57 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2864 helix: 2.03 (0.13), residues: 1684 sheet: -0.32 (0.35), residues: 217 loop : -0.46 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A4159 TYR 0.015 0.001 TYR A1546 PHE 0.024 0.001 PHE A3149 TRP 0.023 0.001 TRP A4387 HIS 0.004 0.000 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00242 (23408) covalent geometry : angle 0.51722 (31790) hydrogen bonds : bond 0.03294 ( 1376) hydrogen bonds : angle 3.86688 ( 4035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 1490 TRP cc_start: 0.7768 (m100) cc_final: 0.7544 (m100) REVERT: A 1491 ASP cc_start: 0.8496 (p0) cc_final: 0.7977 (t0) REVERT: A 1507 MET cc_start: 0.7691 (tmm) cc_final: 0.7352 (tmm) REVERT: A 1523 TRP cc_start: 0.7345 (m100) cc_final: 0.6611 (m100) REVERT: A 1533 LEU cc_start: 0.8725 (mm) cc_final: 0.7836 (tt) REVERT: A 1580 LYS cc_start: 0.7660 (ttpt) cc_final: 0.7233 (mptt) REVERT: A 1877 ASP cc_start: 0.8310 (m-30) cc_final: 0.8040 (m-30) REVERT: A 2074 LYS cc_start: 0.8547 (tptt) cc_final: 0.8103 (ttpt) REVERT: A 2163 ASP cc_start: 0.8722 (t0) cc_final: 0.8178 (m-30) REVERT: A 2187 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8437 (tm-30) REVERT: A 2446 ILE cc_start: 0.9062 (tp) cc_final: 0.8801 (tp) REVERT: A 2874 SER cc_start: 0.8914 (t) cc_final: 0.8453 (p) REVERT: A 3077 ASP cc_start: 0.8584 (t0) cc_final: 0.8282 (m-30) REVERT: A 3500 MET cc_start: 0.9071 (mmm) cc_final: 0.8150 (tpp) REVERT: A 3506 ASP cc_start: 0.8604 (t0) cc_final: 0.8195 (t0) REVERT: A 3683 ASP cc_start: 0.8430 (t0) cc_final: 0.8089 (t0) REVERT: A 3815 MET cc_start: 0.8602 (ttt) cc_final: 0.8344 (ttt) REVERT: A 3862 ASP cc_start: 0.8484 (m-30) cc_final: 0.8117 (t0) REVERT: A 4425 GLN cc_start: 0.8746 (pt0) cc_final: 0.8296 (tp40) outliers start: 19 outliers final: 13 residues processed: 260 average time/residue: 0.1597 time to fit residues: 67.8330 Evaluate side-chains 242 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 258 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 280 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2998 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102566 restraints weight = 42330.157| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.68 r_work: 0.3277 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23408 Z= 0.102 Angle : 0.505 8.083 31790 Z= 0.248 Chirality : 0.038 0.167 3638 Planarity : 0.004 0.046 4057 Dihedral : 5.572 131.342 3188 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.18 % Allowed : 11.75 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.69 (0.16), residues: 2864 helix: 2.16 (0.13), residues: 1687 sheet: -0.31 (0.35), residues: 217 loop : -0.41 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1621 TYR 0.014 0.001 TYR A1546 PHE 0.018 0.001 PHE A3149 TRP 0.024 0.001 TRP A4387 HIS 0.004 0.000 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00226 (23408) covalent geometry : angle 0.50475 (31790) hydrogen bonds : bond 0.03148 ( 1376) hydrogen bonds : angle 3.73525 ( 4035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 259 time to evaluate : 0.998 Fit side-chains REVERT: A 1490 TRP cc_start: 0.7731 (m100) cc_final: 0.7466 (m100) REVERT: A 1491 ASP cc_start: 0.8533 (p0) cc_final: 0.8034 (t0) REVERT: A 1507 MET cc_start: 0.7722 (tmm) cc_final: 0.7385 (tmm) REVERT: A 1523 TRP cc_start: 0.7356 (m100) cc_final: 0.6588 (m100) REVERT: A 1533 LEU cc_start: 0.8785 (mm) cc_final: 0.7877 (tt) REVERT: A 1534 PHE cc_start: 0.7134 (m-80) cc_final: 0.6794 (m-80) REVERT: A 1580 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7229 (mptt) REVERT: A 1877 ASP cc_start: 0.8298 (m-30) cc_final: 0.8023 (m-30) REVERT: A 2074 LYS cc_start: 0.8540 (tptt) cc_final: 0.8093 (ttpt) REVERT: A 2163 ASP cc_start: 0.8717 (t0) cc_final: 0.8286 (m-30) REVERT: A 2187 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 2446 ILE cc_start: 0.9046 (tp) cc_final: 0.8781 (tp) REVERT: A 2874 SER cc_start: 0.8881 (t) cc_final: 0.8411 (p) REVERT: A 3077 ASP cc_start: 0.8574 (t0) cc_final: 0.8289 (m-30) REVERT: A 3500 MET cc_start: 0.9084 (mmm) cc_final: 0.8108 (tpp) REVERT: A 3506 ASP cc_start: 0.8562 (t0) cc_final: 0.8200 (t0) REVERT: A 3628 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.8439 (mmm-85) REVERT: A 3683 ASP cc_start: 0.8417 (t0) cc_final: 0.8061 (t0) REVERT: A 3815 MET cc_start: 0.8734 (ttt) cc_final: 0.8484 (ttt) REVERT: A 3862 ASP cc_start: 0.8487 (m-30) cc_final: 0.8116 (t0) REVERT: A 4425 GLN cc_start: 0.8697 (pt0) cc_final: 0.8261 (tp40) outliers start: 29 outliers final: 19 residues processed: 276 average time/residue: 0.1583 time to fit residues: 71.3834 Evaluate side-chains 257 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 101 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4119 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.125012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098145 restraints weight = 42148.842| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.46 r_work: 0.3235 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23408 Z= 0.164 Angle : 0.557 8.203 31790 Z= 0.272 Chirality : 0.040 0.149 3638 Planarity : 0.004 0.046 4057 Dihedral : 5.655 133.742 3188 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.50 % Allowed : 12.65 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.74 (0.16), residues: 2864 helix: 2.22 (0.13), residues: 1680 sheet: -0.31 (0.34), residues: 226 loop : -0.40 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4159 TYR 0.021 0.001 TYR A3836 PHE 0.016 0.001 PHE A1926 TRP 0.029 0.001 TRP A4387 HIS 0.006 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00388 (23408) covalent geometry : angle 0.55656 (31790) hydrogen bonds : bond 0.03528 ( 1376) hydrogen bonds : angle 3.79089 ( 4035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 1490 TRP cc_start: 0.7897 (m100) cc_final: 0.7657 (m100) REVERT: A 1491 ASP cc_start: 0.8591 (p0) cc_final: 0.8015 (t0) REVERT: A 1507 MET cc_start: 0.7649 (tmm) cc_final: 0.7299 (tmm) REVERT: A 1523 TRP cc_start: 0.7350 (m100) cc_final: 0.6610 (m100) REVERT: A 1533 LEU cc_start: 0.8837 (mm) cc_final: 0.7800 (tt) REVERT: A 1534 PHE cc_start: 0.7269 (m-80) cc_final: 0.6854 (m-80) REVERT: A 1877 ASP cc_start: 0.8542 (m-30) cc_final: 0.8261 (m-30) REVERT: A 2074 LYS cc_start: 0.8696 (tptt) cc_final: 0.8217 (ttpt) REVERT: A 2163 ASP cc_start: 0.8867 (t0) cc_final: 0.8454 (m-30) REVERT: A 2187 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8635 (tm-30) REVERT: A 2446 ILE cc_start: 0.9143 (tp) cc_final: 0.8862 (tp) REVERT: A 2481 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7071 (tpt) REVERT: A 2874 SER cc_start: 0.8964 (t) cc_final: 0.8403 (p) REVERT: A 3077 ASP cc_start: 0.8684 (t0) cc_final: 0.8346 (m-30) REVERT: A 3500 MET cc_start: 0.9150 (mmm) cc_final: 0.8189 (tpp) REVERT: A 3506 ASP cc_start: 0.8797 (t0) cc_final: 0.8400 (t0) REVERT: A 3628 ARG cc_start: 0.8741 (mmm-85) cc_final: 0.8487 (mmm-85) REVERT: A 3683 ASP cc_start: 0.8603 (t0) cc_final: 0.8289 (t0) REVERT: A 3815 MET cc_start: 0.9068 (ttt) cc_final: 0.8828 (ttt) REVERT: A 3816 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7675 (tp30) REVERT: A 3862 ASP cc_start: 0.8672 (m-30) cc_final: 0.8318 (t0) REVERT: A 4107 MET cc_start: 0.8618 (mmm) cc_final: 0.8321 (mmt) REVERT: A 4425 GLN cc_start: 0.8773 (pt0) cc_final: 0.8279 (tp40) outliers start: 37 outliers final: 21 residues processed: 273 average time/residue: 0.1594 time to fit residues: 71.0410 Evaluate side-chains 255 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2481 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 220 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 206 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099457 restraints weight = 42479.502| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.70 r_work: 0.3231 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23408 Z= 0.124 Angle : 0.538 9.306 31790 Z= 0.261 Chirality : 0.039 0.149 3638 Planarity : 0.004 0.068 4057 Dihedral : 5.623 131.819 3188 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.22 % Allowed : 13.50 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.78 (0.16), residues: 2864 helix: 2.25 (0.13), residues: 1687 sheet: -0.30 (0.35), residues: 216 loop : -0.37 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A4159 TYR 0.018 0.001 TYR A2638 PHE 0.015 0.001 PHE A3149 TRP 0.029 0.001 TRP A4387 HIS 0.004 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00285 (23408) covalent geometry : angle 0.53821 (31790) hydrogen bonds : bond 0.03353 ( 1376) hydrogen bonds : angle 3.72898 ( 4035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 1.033 Fit side-chains REVERT: A 1490 TRP cc_start: 0.7764 (m100) cc_final: 0.7528 (m100) REVERT: A 1491 ASP cc_start: 0.8584 (p0) cc_final: 0.8007 (t0) REVERT: A 1507 MET cc_start: 0.7652 (tmm) cc_final: 0.7309 (tmm) REVERT: A 1523 TRP cc_start: 0.7316 (m100) cc_final: 0.6557 (m100) REVERT: A 1533 LEU cc_start: 0.8697 (mm) cc_final: 0.7792 (tt) REVERT: A 1877 ASP cc_start: 0.8378 (m-30) cc_final: 0.8122 (m-30) REVERT: A 2074 LYS cc_start: 0.8649 (tptt) cc_final: 0.8190 (ttpt) REVERT: A 2163 ASP cc_start: 0.8743 (t0) cc_final: 0.8385 (m-30) REVERT: A 2187 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 2446 ILE cc_start: 0.9067 (tp) cc_final: 0.8782 (tp) REVERT: A 2874 SER cc_start: 0.8867 (t) cc_final: 0.8311 (p) REVERT: A 3077 ASP cc_start: 0.8594 (t0) cc_final: 0.8299 (m-30) REVERT: A 3500 MET cc_start: 0.9086 (mmm) cc_final: 0.8099 (tpp) REVERT: A 3506 ASP cc_start: 0.8627 (t0) cc_final: 0.8244 (t0) REVERT: A 3628 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8465 (mmm-85) REVERT: A 3629 PHE cc_start: 0.8038 (m-10) cc_final: 0.7823 (m-10) REVERT: A 3683 ASP cc_start: 0.8434 (t0) cc_final: 0.8076 (t0) REVERT: A 3815 MET cc_start: 0.8985 (ttt) cc_final: 0.8747 (ttt) REVERT: A 3816 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7441 (tp30) REVERT: A 3862 ASP cc_start: 0.8537 (m-30) cc_final: 0.8167 (t0) REVERT: A 4107 MET cc_start: 0.8451 (mmm) cc_final: 0.8163 (mmt) REVERT: A 4425 GLN cc_start: 0.8722 (pt0) cc_final: 0.8260 (tp40) outliers start: 30 outliers final: 20 residues processed: 260 average time/residue: 0.1625 time to fit residues: 69.2642 Evaluate side-chains 253 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 202 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 222 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098655 restraints weight = 42295.333| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.65 r_work: 0.3239 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23408 Z= 0.123 Angle : 0.536 9.553 31790 Z= 0.260 Chirality : 0.039 0.204 3638 Planarity : 0.004 0.046 4057 Dihedral : 5.579 131.321 3188 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.38 % Allowed : 13.66 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.84 (0.16), residues: 2864 helix: 2.27 (0.13), residues: 1687 sheet: -0.38 (0.34), residues: 232 loop : -0.26 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A4159 TYR 0.021 0.001 TYR A3836 PHE 0.014 0.001 PHE A1568 TRP 0.034 0.001 TRP A4387 HIS 0.004 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00284 (23408) covalent geometry : angle 0.53593 (31790) hydrogen bonds : bond 0.03302 ( 1376) hydrogen bonds : angle 3.70210 ( 4035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.891 Fit side-chains REVERT: A 1490 TRP cc_start: 0.7717 (m100) cc_final: 0.7456 (m100) REVERT: A 1491 ASP cc_start: 0.8567 (p0) cc_final: 0.7958 (t0) REVERT: A 1507 MET cc_start: 0.7588 (tmm) cc_final: 0.7264 (tmm) REVERT: A 1523 TRP cc_start: 0.7310 (m100) cc_final: 0.6547 (m100) REVERT: A 1533 LEU cc_start: 0.8701 (mm) cc_final: 0.7814 (tt) REVERT: A 1877 ASP cc_start: 0.8410 (m-30) cc_final: 0.8163 (m-30) REVERT: A 2074 LYS cc_start: 0.8669 (tptt) cc_final: 0.8209 (ttpt) REVERT: A 2163 ASP cc_start: 0.8734 (t0) cc_final: 0.8395 (m-30) REVERT: A 2187 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 2446 ILE cc_start: 0.9049 (tp) cc_final: 0.8757 (tp) REVERT: A 2874 SER cc_start: 0.8873 (t) cc_final: 0.8324 (p) REVERT: A 3077 ASP cc_start: 0.8584 (t0) cc_final: 0.8293 (m-30) REVERT: A 3199 MET cc_start: 0.7384 (tpp) cc_final: 0.7003 (tpt) REVERT: A 3500 MET cc_start: 0.9086 (mmm) cc_final: 0.8087 (tpp) REVERT: A 3506 ASP cc_start: 0.8619 (t0) cc_final: 0.8238 (t0) REVERT: A 3628 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8454 (mmm-85) REVERT: A 3629 PHE cc_start: 0.8129 (m-10) cc_final: 0.7858 (m-10) REVERT: A 3683 ASP cc_start: 0.8425 (t0) cc_final: 0.8061 (t0) REVERT: A 3791 MET cc_start: 0.7546 (tmm) cc_final: 0.6744 (ptp) REVERT: A 3815 MET cc_start: 0.9009 (ttt) cc_final: 0.8794 (ttt) REVERT: A 3816 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7467 (tp30) REVERT: A 3862 ASP cc_start: 0.8538 (m-30) cc_final: 0.8170 (t0) REVERT: A 4425 GLN cc_start: 0.8735 (pt0) cc_final: 0.8254 (tp40) outliers start: 34 outliers final: 23 residues processed: 265 average time/residue: 0.1487 time to fit residues: 64.6088 Evaluate side-chains 257 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 2481 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 4067 THR Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 280 optimal weight: 9.9990 chunk 137 optimal weight: 0.0270 chunk 150 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 222 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.099052 restraints weight = 42055.091| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.65 r_work: 0.3246 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23408 Z= 0.116 Angle : 0.538 10.439 31790 Z= 0.260 Chirality : 0.039 0.168 3638 Planarity : 0.004 0.078 4057 Dihedral : 5.543 130.810 3188 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.14 % Allowed : 14.44 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.85 (0.16), residues: 2864 helix: 2.30 (0.13), residues: 1687 sheet: -0.54 (0.33), residues: 241 loop : -0.25 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3206 TYR 0.022 0.001 TYR A2638 PHE 0.018 0.001 PHE A2479 TRP 0.038 0.001 TRP A4387 HIS 0.004 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00265 (23408) covalent geometry : angle 0.53828 (31790) hydrogen bonds : bond 0.03242 ( 1376) hydrogen bonds : angle 3.68142 ( 4035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.956 Fit side-chains REVERT: A 1490 TRP cc_start: 0.7725 (m100) cc_final: 0.7472 (m100) REVERT: A 1491 ASP cc_start: 0.8571 (p0) cc_final: 0.7973 (t0) REVERT: A 1507 MET cc_start: 0.7583 (tmm) cc_final: 0.7265 (tmm) REVERT: A 1523 TRP cc_start: 0.7351 (m100) cc_final: 0.6575 (m100) REVERT: A 1533 LEU cc_start: 0.8733 (mm) cc_final: 0.7839 (tt) REVERT: A 1877 ASP cc_start: 0.8317 (m-30) cc_final: 0.8053 (m-30) REVERT: A 2074 LYS cc_start: 0.8677 (tptt) cc_final: 0.8216 (ttpt) REVERT: A 2163 ASP cc_start: 0.8714 (t0) cc_final: 0.8278 (m-30) REVERT: A 2187 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 2446 ILE cc_start: 0.9019 (tp) cc_final: 0.8739 (tp) REVERT: A 2481 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7176 (tpt) REVERT: A 2874 SER cc_start: 0.8867 (t) cc_final: 0.8341 (p) REVERT: A 3077 ASP cc_start: 0.8574 (t0) cc_final: 0.8286 (m-30) REVERT: A 3199 MET cc_start: 0.7423 (tpp) cc_final: 0.7057 (tpt) REVERT: A 3500 MET cc_start: 0.9089 (mmm) cc_final: 0.8099 (tpp) REVERT: A 3506 ASP cc_start: 0.8625 (t0) cc_final: 0.8241 (t0) REVERT: A 3628 ARG cc_start: 0.8705 (mmm-85) cc_final: 0.8455 (mmm-85) REVERT: A 3629 PHE cc_start: 0.8164 (m-10) cc_final: 0.7873 (m-10) REVERT: A 3683 ASP cc_start: 0.8405 (t0) cc_final: 0.8038 (t0) REVERT: A 3791 MET cc_start: 0.7541 (tmm) cc_final: 0.6825 (ptp) REVERT: A 3815 MET cc_start: 0.9025 (ttt) cc_final: 0.8808 (ttt) REVERT: A 3816 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7490 (tp30) REVERT: A 3862 ASP cc_start: 0.8523 (m-30) cc_final: 0.8155 (t0) REVERT: A 4425 GLN cc_start: 0.8746 (pt0) cc_final: 0.8269 (tp40) outliers start: 28 outliers final: 21 residues processed: 263 average time/residue: 0.1573 time to fit residues: 67.3325 Evaluate side-chains 259 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 2481 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3055 THR Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 202 optimal weight: 0.8980 chunk 194 optimal weight: 0.0670 chunk 215 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 119 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.127761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.100592 restraints weight = 42127.579| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.64 r_work: 0.3266 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23408 Z= 0.101 Angle : 0.540 11.296 31790 Z= 0.258 Chirality : 0.038 0.163 3638 Planarity : 0.003 0.048 4057 Dihedral : 5.471 129.287 3188 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.89 % Allowed : 14.80 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.89 (0.16), residues: 2864 helix: 2.34 (0.13), residues: 1687 sheet: -0.56 (0.33), residues: 242 loop : -0.23 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4159 TYR 0.023 0.001 TYR A2638 PHE 0.015 0.001 PHE A3813 TRP 0.041 0.001 TRP A4387 HIS 0.003 0.000 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00222 (23408) covalent geometry : angle 0.53988 (31790) hydrogen bonds : bond 0.03112 ( 1376) hydrogen bonds : angle 3.64572 ( 4035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.943 Fit side-chains REVERT: A 1490 TRP cc_start: 0.7609 (m100) cc_final: 0.7395 (m100) REVERT: A 1491 ASP cc_start: 0.8566 (p0) cc_final: 0.8279 (p0) REVERT: A 1507 MET cc_start: 0.7633 (tmm) cc_final: 0.7328 (tmm) REVERT: A 1523 TRP cc_start: 0.7343 (m100) cc_final: 0.6564 (m100) REVERT: A 1533 LEU cc_start: 0.8806 (mm) cc_final: 0.7944 (tt) REVERT: A 1877 ASP cc_start: 0.8335 (m-30) cc_final: 0.8068 (m-30) REVERT: A 2074 LYS cc_start: 0.8653 (tptt) cc_final: 0.8189 (ttpt) REVERT: A 2163 ASP cc_start: 0.8697 (t0) cc_final: 0.8287 (m-30) REVERT: A 2187 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8476 (tm-30) REVERT: A 2481 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7241 (tpt) REVERT: A 2522 THR cc_start: 0.8757 (t) cc_final: 0.8539 (t) REVERT: A 2874 SER cc_start: 0.8840 (t) cc_final: 0.8333 (p) REVERT: A 2953 MET cc_start: 0.7462 (ttm) cc_final: 0.7174 (mtp) REVERT: A 3077 ASP cc_start: 0.8562 (t0) cc_final: 0.8274 (m-30) REVERT: A 3155 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.8137 (m-70) REVERT: A 3199 MET cc_start: 0.7389 (tpp) cc_final: 0.7026 (tpt) REVERT: A 3500 MET cc_start: 0.9091 (mmm) cc_final: 0.8092 (tpp) REVERT: A 3506 ASP cc_start: 0.8583 (t0) cc_final: 0.8227 (t0) REVERT: A 3628 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8432 (mmm-85) REVERT: A 3629 PHE cc_start: 0.8123 (m-10) cc_final: 0.7849 (m-10) REVERT: A 3683 ASP cc_start: 0.8386 (t0) cc_final: 0.8088 (t0) REVERT: A 3791 MET cc_start: 0.7483 (tmm) cc_final: 0.6836 (ptp) REVERT: A 3816 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7465 (tp30) REVERT: A 3862 ASP cc_start: 0.8456 (m-30) cc_final: 0.8103 (t0) REVERT: A 4425 GLN cc_start: 0.8741 (pt0) cc_final: 0.8270 (tp40) outliers start: 22 outliers final: 18 residues processed: 261 average time/residue: 0.1658 time to fit residues: 70.5525 Evaluate side-chains 257 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 2481 MET Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 248 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 136 optimal weight: 0.0040 chunk 250 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 224 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102266 restraints weight = 42382.813| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.71 r_work: 0.3269 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23408 Z= 0.101 Angle : 0.541 11.077 31790 Z= 0.259 Chirality : 0.039 0.236 3638 Planarity : 0.004 0.068 4057 Dihedral : 5.400 128.495 3188 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.85 % Allowed : 15.21 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.94 (0.16), residues: 2864 helix: 2.39 (0.13), residues: 1681 sheet: -0.39 (0.33), residues: 245 loop : -0.27 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3206 TYR 0.021 0.001 TYR A2638 PHE 0.018 0.001 PHE A2479 TRP 0.045 0.001 TRP A4387 HIS 0.011 0.001 HIS A3822 Details of bonding type rmsd covalent geometry : bond 0.00221 (23408) covalent geometry : angle 0.54123 (31790) hydrogen bonds : bond 0.03082 ( 1376) hydrogen bonds : angle 3.60415 ( 4035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 1491 ASP cc_start: 0.8573 (p0) cc_final: 0.8289 (p0) REVERT: A 1507 MET cc_start: 0.7633 (tmm) cc_final: 0.7340 (tmm) REVERT: A 1523 TRP cc_start: 0.7368 (m100) cc_final: 0.6584 (m100) REVERT: A 1533 LEU cc_start: 0.8821 (mm) cc_final: 0.7948 (tt) REVERT: A 1877 ASP cc_start: 0.8329 (m-30) cc_final: 0.8064 (m-30) REVERT: A 2074 LYS cc_start: 0.8641 (tptt) cc_final: 0.8166 (ttpt) REVERT: A 2163 ASP cc_start: 0.8676 (t0) cc_final: 0.8299 (m-30) REVERT: A 2187 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8489 (tm-30) REVERT: A 2481 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7220 (tpt) REVERT: A 2522 THR cc_start: 0.8759 (t) cc_final: 0.8545 (t) REVERT: A 2874 SER cc_start: 0.8795 (t) cc_final: 0.8328 (p) REVERT: A 2953 MET cc_start: 0.7455 (ttm) cc_final: 0.7175 (mtp) REVERT: A 3077 ASP cc_start: 0.8549 (t0) cc_final: 0.8273 (m-30) REVERT: A 3155 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8185 (m-70) REVERT: A 3199 MET cc_start: 0.7437 (tpp) cc_final: 0.7074 (tpt) REVERT: A 3500 MET cc_start: 0.9083 (mmm) cc_final: 0.8062 (tpp) REVERT: A 3506 ASP cc_start: 0.8573 (t0) cc_final: 0.8220 (t0) REVERT: A 3628 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8431 (mmm-85) REVERT: A 3629 PHE cc_start: 0.8080 (m-10) cc_final: 0.7807 (m-10) REVERT: A 3683 ASP cc_start: 0.8350 (t0) cc_final: 0.8054 (t0) REVERT: A 3791 MET cc_start: 0.7498 (tmm) cc_final: 0.7024 (ptp) REVERT: A 3816 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7407 (tp30) REVERT: A 3862 ASP cc_start: 0.8460 (m-30) cc_final: 0.8035 (t0) REVERT: A 4425 GLN cc_start: 0.8749 (pt0) cc_final: 0.8265 (tp40) outliers start: 21 outliers final: 17 residues processed: 268 average time/residue: 0.1641 time to fit residues: 70.7876 Evaluate side-chains 260 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 2481 MET Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2668 LEU Chi-restraints excluded: chain A residue 2787 ASP Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3193 GLU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 162 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 223 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101671 restraints weight = 42246.499| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.71 r_work: 0.3267 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23408 Z= 0.110 Angle : 0.548 10.691 31790 Z= 0.263 Chirality : 0.039 0.221 3638 Planarity : 0.004 0.049 4057 Dihedral : 5.378 128.766 3188 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.89 % Allowed : 15.53 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.94 (0.16), residues: 2864 helix: 2.39 (0.13), residues: 1681 sheet: -0.43 (0.33), residues: 246 loop : -0.26 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2113 TYR 0.022 0.001 TYR A2638 PHE 0.020 0.001 PHE A3813 TRP 0.043 0.001 TRP A4387 HIS 0.010 0.001 HIS A3822 Details of bonding type rmsd covalent geometry : bond 0.00251 (23408) covalent geometry : angle 0.54777 (31790) hydrogen bonds : bond 0.03106 ( 1376) hydrogen bonds : angle 3.61636 ( 4035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5654.04 seconds wall clock time: 97 minutes 42.96 seconds (5862.96 seconds total)