Starting phenix.real_space_refine on Sun Mar 17 03:54:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/03_2024/7z8l_14556_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/03_2024/7z8l_14556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/03_2024/7z8l_14556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/03_2024/7z8l_14556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/03_2024/7z8l_14556_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/03_2024/7z8l_14556_updated.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 C 9809 2.51 5 N 3333 2.21 5 O 3359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16513 Number of models: 1 Model: "" Number of chains: 3 Chain: "f" Number of atoms: 15087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3047, 15087 Classifications: {'peptide': 3047} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2709} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2913} Chain breaks: 3 Unresolved chain link angles: 133 Unresolved non-hydrogen bonds: 9971 Unresolved non-hydrogen angles: 12793 Unresolved non-hydrogen dihedrals: 8310 Unresolved non-hydrogen chiralities: 911 Planarities with less than four sites: {'GLN:plan1': 158, 'HIS:plan': 65, 'GLU%COO:plan': 1, 'TYR:plan': 83, 'ASN:plan1': 123, 'TRP:plan': 55, 'ASP:plan': 163, 'PHE:plan': 132, 'GLU:plan': 229, 'ARG:plan': 186} Unresolved non-hydrogen planarities: 5533 Chain: "q" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1305 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 236} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 894 Unresolved non-hydrogen angles: 1148 Unresolved non-hydrogen dihedrals: 759 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 10, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 12, 'PHE:plan': 12, 'GLU:plan': 22, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 487 Chain: "f" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 121 Unusual residues: {' MG': 1, 'ADP': 1, 'ANP': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 9.62, per 1000 atoms: 0.58 Number of scatterers: 16513 At special positions: 0 Unit cell: (140.609, 175.252, 165.063, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) P 11 15.00 Mg 1 11.99 O 3359 8.00 N 3333 7.00 C 9809 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 - 3.50 Amino acid : False - 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: 8.27 Conformation dependent library (CDL) restraints added in 5.0 seconds 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6294 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 20 sheets defined 54.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.76 Creating SS restraints... Processing helix chain 'f' and resid 1328 through 1347 removed outlier: 4.177A pdb=" N LYS f1338 " --> pdb=" O SER f1334 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL f1339 " --> pdb=" O GLU f1335 " (cutoff:3.500A) Processing helix chain 'f' and resid 1351 through 1353 No H-bonds generated for 'chain 'f' and resid 1351 through 1353' Processing helix chain 'f' and resid 1356 through 1372 removed outlier: 3.619A pdb=" N SER f1372 " --> pdb=" O ASN f1368 " (cutoff:3.500A) Processing helix chain 'f' and resid 1375 through 1379 removed outlier: 3.676A pdb=" N GLN f1379 " --> pdb=" O ALA f1375 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 1375 through 1379' Processing helix chain 'f' and resid 1381 through 1404 removed outlier: 4.441A pdb=" N MET f1398 " --> pdb=" O MET f1394 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU f1399 " --> pdb=" O LYS f1395 " (cutoff:3.500A) Processing helix chain 'f' and resid 1410 through 1420 Processing helix chain 'f' and resid 1431 through 1436 Processing helix chain 'f' and resid 1443 through 1471 Processing helix chain 'f' and resid 1490 through 1509 removed outlier: 3.858A pdb=" N LEU f1509 " --> pdb=" O SER f1505 " (cutoff:3.500A) Processing helix chain 'f' and resid 1513 through 1551 removed outlier: 3.518A pdb=" N GLU f1517 " --> pdb=" O LYS f1514 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU f1518 " --> pdb=" O VAL f1515 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASP f1535 " --> pdb=" O ALA f1532 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE f1538 " --> pdb=" O ASP f1535 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG f1543 " --> pdb=" O VAL f1540 " (cutoff:3.500A) Processing helix chain 'f' and resid 1557 through 1560 No H-bonds generated for 'chain 'f' and resid 1557 through 1560' Processing helix chain 'f' and resid 1562 through 1583 removed outlier: 3.618A pdb=" N GLU f1574 " --> pdb=" O SER f1570 " (cutoff:3.500A) Processing helix chain 'f' and resid 1588 through 1592 Processing helix chain 'f' and resid 1597 through 1625 Processing helix chain 'f' and resid 1627 through 1631 Processing helix chain 'f' and resid 1634 through 1642 Processing helix chain 'f' and resid 1647 through 1657 removed outlier: 4.025A pdb=" N LYS f1652 " --> pdb=" O LYS f1649 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE f1654 " --> pdb=" O GLN f1651 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS f1655 " --> pdb=" O LYS f1652 " (cutoff:3.500A) Processing helix chain 'f' and resid 1698 through 1728 removed outlier: 4.243A pdb=" N ILE f1726 " --> pdb=" O THR f1722 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE f1727 " --> pdb=" O GLU f1723 " (cutoff:3.500A) Processing helix chain 'f' and resid 1735 through 1744 Processing helix chain 'f' and resid 1747 through 1769 Processing helix chain 'f' and resid 1776 through 1797 removed outlier: 3.536A pdb=" N LEU f1797 " --> pdb=" O ALA f1793 " (cutoff:3.500A) Processing helix chain 'f' and resid 1802 through 1828 removed outlier: 3.635A pdb=" N HIS f1817 " --> pdb=" O THR f1813 " (cutoff:3.500A) Processing helix chain 'f' and resid 1836 through 1839 No H-bonds generated for 'chain 'f' and resid 1836 through 1839' Processing helix chain 'f' and resid 1883 through 1897 Processing helix chain 'f' and resid 1912 through 1922 Processing helix chain 'f' and resid 1941 through 1951 Processing helix chain 'f' and resid 1960 through 1962 No H-bonds generated for 'chain 'f' and resid 1960 through 1962' Processing helix chain 'f' and resid 1965 through 1985 removed outlier: 3.896A pdb=" N HIS f1985 " --> pdb=" O ALA f1981 " (cutoff:3.500A) Processing helix chain 'f' and resid 2046 through 2056 Processing helix chain 'f' and resid 2063 through 2079 Proline residue: f2071 - end of helix removed outlier: 3.532A pdb=" N LYS f2074 " --> pdb=" O VAL f2070 " (cutoff:3.500A) Processing helix chain 'f' and resid 2090 through 2117 Processing helix chain 'f' and resid 2124 through 2129 Processing helix chain 'f' and resid 2133 through 2148 Proline residue: f2147 - end of helix Processing helix chain 'f' and resid 2151 through 2164 Proline residue: f2155 - end of helix Processing helix chain 'f' and resid 2176 through 2188 Processing helix chain 'f' and resid 2201 through 2216 Processing helix chain 'f' and resid 2230 through 2245 removed outlier: 3.726A pdb=" N ARG f2243 " --> pdb=" O LYS f2239 " (cutoff:3.500A) Processing helix chain 'f' and resid 2261 through 2265 Processing helix chain 'f' and resid 2279 through 2289 Processing helix chain 'f' and resid 2310 through 2319 removed outlier: 3.793A pdb=" N GLU f2313 " --> pdb=" O GLU f2310 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN f2314 " --> pdb=" O TRP f2311 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER f2317 " --> pdb=" O ASN f2314 " (cutoff:3.500A) Processing helix chain 'f' and resid 2353 through 2358 removed outlier: 3.564A pdb=" N ARG f2358 " --> pdb=" O ALA f2354 " (cutoff:3.500A) Processing helix chain 'f' and resid 2366 through 2368 No H-bonds generated for 'chain 'f' and resid 2366 through 2368' Processing helix chain 'f' and resid 2371 through 2384 removed outlier: 3.601A pdb=" N SER f2384 " --> pdb=" O ALA f2380 " (cutoff:3.500A) Processing helix chain 'f' and resid 2394 through 2399 removed outlier: 4.201A pdb=" N ARG f2398 " --> pdb=" O ALA f2394 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS f2399 " --> pdb=" O GLN f2395 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 2394 through 2399' Processing helix chain 'f' and resid 2411 through 2427 Proline residue: f2425 - end of helix Processing helix chain 'f' and resid 2432 through 2442 removed outlier: 3.658A pdb=" N GLN f2442 " --> pdb=" O GLU f2438 " (cutoff:3.500A) Processing helix chain 'f' and resid 2451 through 2475 Processing helix chain 'f' and resid 2483 through 2505 removed outlier: 3.562A pdb=" N VAL f2495 " --> pdb=" O GLN f2491 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY f2504 " --> pdb=" O TRP f2500 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP f2505 " --> pdb=" O SER f2501 " (cutoff:3.500A) Processing helix chain 'f' and resid 2508 through 2521 Processing helix chain 'f' and resid 2534 through 2536 No H-bonds generated for 'chain 'f' and resid 2534 through 2536' Processing helix chain 'f' and resid 2548 through 2551 Processing helix chain 'f' and resid 2572 through 2586 Processing helix chain 'f' and resid 2601 through 2611 Processing helix chain 'f' and resid 2628 through 2638 Processing helix chain 'f' and resid 2678 through 2689 Processing helix chain 'f' and resid 2725 through 2728 No H-bonds generated for 'chain 'f' and resid 2725 through 2728' Processing helix chain 'f' and resid 2740 through 2758 removed outlier: 3.631A pdb=" N ARG f2757 " --> pdb=" O ARG f2753 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU f2758 " --> pdb=" O ALA f2754 " (cutoff:3.500A) Processing helix chain 'f' and resid 2763 through 2783 removed outlier: 4.429A pdb=" N GLU f2767 " --> pdb=" O THR f2764 " (cutoff:3.500A) Proline residue: f2768 - end of helix removed outlier: 3.664A pdb=" N ALA f2771 " --> pdb=" O PRO f2768 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE f2776 " --> pdb=" O MET f2773 " (cutoff:3.500A) Processing helix chain 'f' and resid 2796 through 2811 Processing helix chain 'f' and resid 2818 through 2833 Processing helix chain 'f' and resid 2840 through 2857 removed outlier: 3.604A pdb=" N ASP f2851 " --> pdb=" O ASP f2847 " (cutoff:3.500A) Processing helix chain 'f' and resid 2863 through 2866 No H-bonds generated for 'chain 'f' and resid 2863 through 2866' Processing helix chain 'f' and resid 2886 through 2902 removed outlier: 3.983A pdb=" N GLU f2902 " --> pdb=" O LYS f2898 " (cutoff:3.500A) Processing helix chain 'f' and resid 2913 through 2927 removed outlier: 3.994A pdb=" N ASP f2917 " --> pdb=" O ASN f2913 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS f2918 " --> pdb=" O GLU f2914 " (cutoff:3.500A) Processing helix chain 'f' and resid 2946 through 2953 Processing helix chain 'f' and resid 2969 through 2984 Processing helix chain 'f' and resid 3003 through 3005 No H-bonds generated for 'chain 'f' and resid 3003 through 3005' Processing helix chain 'f' and resid 3007 through 3014 removed outlier: 3.889A pdb=" N LEU f3011 " --> pdb=" O ARG f3007 " (cutoff:3.500A) Processing helix chain 'f' and resid 3024 through 3040 Processing helix chain 'f' and resid 3047 through 3061 Processing helix chain 'f' and resid 3083 through 3088 Processing helix chain 'f' and resid 3099 through 3107 Processing helix chain 'f' and resid 3139 through 3163 removed outlier: 3.699A pdb=" N HIS f3151 " --> pdb=" O CYS f3147 " (cutoff:3.500A) Processing helix chain 'f' and resid 3173 through 3220 Processing helix chain 'f' and resid 3471 through 3515 removed outlier: 3.599A pdb=" N SER f3475 " --> pdb=" O LYS f3471 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR f3476 " --> pdb=" O VAL f3472 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA f3477 " --> pdb=" O ASN f3473 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA f3484 " --> pdb=" O LYS f3480 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA f3504 " --> pdb=" O MET f3500 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLY f3505 " --> pdb=" O SER f3501 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP f3506 " --> pdb=" O THR f3502 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE f3513 " --> pdb=" O LEU f3509 " (cutoff:3.500A) Processing helix chain 'f' and resid 3522 through 3538 Processing helix chain 'f' and resid 3549 through 3552 No H-bonds generated for 'chain 'f' and resid 3549 through 3552' Processing helix chain 'f' and resid 3556 through 3564 Processing helix chain 'f' and resid 3571 through 3579 Processing helix chain 'f' and resid 3595 through 3603 Processing helix chain 'f' and resid 3605 through 3607 No H-bonds generated for 'chain 'f' and resid 3605 through 3607' Processing helix chain 'f' and resid 3617 through 3629 removed outlier: 4.503A pdb=" N ARG f3620 " --> pdb=" O ASP f3617 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS f3621 " --> pdb=" O ALA f3618 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE f3629 " --> pdb=" O ALA f3626 " (cutoff:3.500A) Processing helix chain 'f' and resid 3638 through 3640 No H-bonds generated for 'chain 'f' and resid 3638 through 3640' Processing helix chain 'f' and resid 3643 through 3650 Proline residue: f3647 - end of helix Processing helix chain 'f' and resid 3690 through 3694 removed outlier: 3.519A pdb=" N SER f3694 " --> pdb=" O PRO f3690 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 3690 through 3694' Processing helix chain 'f' and resid 3705 through 3720 Processing helix chain 'f' and resid 3722 through 3729 Processing helix chain 'f' and resid 3736 through 3751 Processing helix chain 'f' and resid 3766 through 3787 removed outlier: 3.763A pdb=" N ASN f3772 " --> pdb=" O THR f3769 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU f3773 " --> pdb=" O LEU f3770 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG f3775 " --> pdb=" O ASN f3772 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU f3776 " --> pdb=" O LEU f3773 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA f3777 " --> pdb=" O LYS f3774 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS f3783 " --> pdb=" O VAL f3780 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL f3784 " --> pdb=" O THR f3781 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR f3787 " --> pdb=" O VAL f3784 " (cutoff:3.500A) Processing helix chain 'f' and resid 3789 through 3800 removed outlier: 3.597A pdb=" N GLN f3800 " --> pdb=" O THR f3796 " (cutoff:3.500A) Processing helix chain 'f' and resid 3802 through 3820 removed outlier: 4.537A pdb=" N LYS f3819 " --> pdb=" O MET f3815 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN f3820 " --> pdb=" O GLU f3816 " (cutoff:3.500A) Processing helix chain 'f' and resid 3829 through 3840 Processing helix chain 'f' and resid 3844 through 3846 No H-bonds generated for 'chain 'f' and resid 3844 through 3846' Processing helix chain 'f' and resid 3852 through 3874 removed outlier: 4.147A pdb=" N GLY f3874 " --> pdb=" O ARG f3870 " (cutoff:3.500A) Processing helix chain 'f' and resid 3877 through 3894 removed outlier: 4.728A pdb=" N ILE f3881 " --> pdb=" O HIS f3877 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR f3882 " --> pdb=" O GLN f3878 " (cutoff:3.500A) Processing helix chain 'f' and resid 3902 through 3910 Processing helix chain 'f' and resid 3929 through 3940 removed outlier: 3.822A pdb=" N CYS f3940 " --> pdb=" O VAL f3936 " (cutoff:3.500A) Processing helix chain 'f' and resid 3947 through 3953 Processing helix chain 'f' and resid 3955 through 3961 removed outlier: 4.286A pdb=" N GLY f3958 " --> pdb=" O GLU f3955 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE f3959 " --> pdb=" O GLN f3956 " (cutoff:3.500A) Processing helix chain 'f' and resid 3966 through 3969 Processing helix chain 'f' and resid 3982 through 3996 Processing helix chain 'f' and resid 3998 through 4012 removed outlier: 4.833A pdb=" N LEU f4002 " --> pdb=" O ASP f3999 " (cutoff:3.500A) Processing helix chain 'f' and resid 4027 through 4033 Processing helix chain 'f' and resid 4052 through 4062 Processing helix chain 'f' and resid 4074 through 4090 removed outlier: 3.653A pdb=" N ASN f4078 " --> pdb=" O ALA f4074 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS f4089 " --> pdb=" O ASN f4085 " (cutoff:3.500A) Processing helix chain 'f' and resid 4099 through 4101 No H-bonds generated for 'chain 'f' and resid 4099 through 4101' Processing helix chain 'f' and resid 4103 through 4115 removed outlier: 3.781A pdb=" N SER f4115 " --> pdb=" O LYS f4111 " (cutoff:3.500A) Processing helix chain 'f' and resid 4136 through 4140 Processing helix chain 'f' and resid 4153 through 4163 Processing helix chain 'f' and resid 4166 through 4170 Processing helix chain 'f' and resid 4174 through 4196 removed outlier: 3.783A pdb=" N ALA f4177 " --> pdb=" O ASN f4174 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE f4190 " --> pdb=" O HIS f4187 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU f4192 " --> pdb=" O ILE f4189 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG f4193 " --> pdb=" O ILE f4190 " (cutoff:3.500A) Processing helix chain 'f' and resid 4209 through 4227 Processing helix chain 'f' and resid 4240 through 4249 Processing helix chain 'f' and resid 4259 through 4272 Processing helix chain 'f' and resid 4275 through 4278 Processing helix chain 'f' and resid 4288 through 4290 No H-bonds generated for 'chain 'f' and resid 4288 through 4290' Processing helix chain 'f' and resid 4302 through 4310 Processing helix chain 'f' and resid 4318 through 4320 No H-bonds generated for 'chain 'f' and resid 4318 through 4320' Processing helix chain 'f' and resid 4325 through 4346 removed outlier: 3.981A pdb=" N LEU f4332 " --> pdb=" O ARG f4329 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER f4341 " --> pdb=" O ASP f4338 " (cutoff:3.500A) Processing helix chain 'f' and resid 4376 through 4390 removed outlier: 3.737A pdb=" N THR f4382 " --> pdb=" O ARG f4378 " (cutoff:3.500A) Processing helix chain 'f' and resid 4402 through 4406 removed outlier: 4.212A pdb=" N LYS f4406 " --> pdb=" O VAL f4402 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 4402 through 4406' Processing helix chain 'f' and resid 4408 through 4438 Processing helix chain 'f' and resid 4446 through 4457 Processing helix chain 'f' and resid 4462 through 4464 No H-bonds generated for 'chain 'f' and resid 4462 through 4464' Processing helix chain 'f' and resid 4475 through 4506 removed outlier: 7.447A pdb=" N ALA f4501 " --> pdb=" O ALA f4497 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LYS f4502 " --> pdb=" O SER f4498 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU f4503 " --> pdb=" O GLY f4499 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU f4504 " --> pdb=" O GLY f4500 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS f4505 " --> pdb=" O ALA f4501 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN f4506 " --> pdb=" O LYS f4502 " (cutoff:3.500A) Processing helix chain 'f' and resid 4511 through 4513 No H-bonds generated for 'chain 'f' and resid 4511 through 4513' Processing helix chain 'f' and resid 4517 through 4532 Processing helix chain 'f' and resid 4632 through 4637 Processing helix chain 'q' and resid 67 through 74 Processing helix chain 'q' and resid 113 through 121 removed outlier: 4.326A pdb=" N GLY q 117 " --> pdb=" O TYR q 114 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS q 120 " --> pdb=" O GLY q 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 128 through 130 No H-bonds generated for 'chain 'q' and resid 128 through 130' Processing helix chain 'q' and resid 142 through 163 removed outlier: 5.877A pdb=" N MET q 146 " --> pdb=" O TRP q 143 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU q 147 " --> pdb=" O THR q 144 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP q 152 " --> pdb=" O LEU q 149 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA q 153 " --> pdb=" O GLN q 150 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP q 161 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Processing helix chain 'q' and resid 167 through 182 Processing helix chain 'q' and resid 234 through 243 removed outlier: 4.595A pdb=" N GLU q 241 " --> pdb=" O SER q 238 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU q 243 " --> pdb=" O LEU q 240 " (cutoff:3.500A) Processing helix chain 'q' and resid 248 through 265 Processing helix chain 'q' and resid 280 through 292 Processing helix chain 'q' and resid 317 through 326 removed outlier: 3.734A pdb=" N ILE q 322 " --> pdb=" O LYS q 318 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU q 323 " --> pdb=" O LYS q 319 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS q 324 " --> pdb=" O ILE q 320 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU q 325 " --> pdb=" O ALA q 321 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN q 326 " --> pdb=" O ILE q 322 " (cutoff:3.500A) Processing helix chain 'q' and resid 336 through 339 No H-bonds generated for 'chain 'q' and resid 336 through 339' Processing sheet with id= A, first strand: chain 'f' and resid 1477 through 1480 removed outlier: 3.822A pdb=" N CYS f1484 " --> pdb=" O TYR f1480 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'f' and resid 1683 through 1685 removed outlier: 6.556A pdb=" N ILE f1665 " --> pdb=" O LEU f1674 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE f1676 " --> pdb=" O SER f1663 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER f1663 " --> pdb=" O ILE f1676 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'f' and resid 1843 through 1846 Processing sheet with id= D, first strand: chain 'f' and resid 1901 through 1905 Processing sheet with id= E, first strand: chain 'f' and resid 1927 through 1931 removed outlier: 6.910A pdb=" N TRP f1954 " --> pdb=" O LEU f1928 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE f1930 " --> pdb=" O TRP f1954 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS f1956 " --> pdb=" O PHE f1930 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA f2013 " --> pdb=" O GLY f1955 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N PHE f1957 " --> pdb=" O ALA f2013 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE f2015 " --> pdb=" O PHE f1957 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'f' and resid 1998 through 2001 Processing sheet with id= G, first strand: chain 'f' and resid 2360 through 2362 removed outlier: 8.756A pdb=" N LEU f2220 " --> pdb=" O VAL f2339 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE f2341 " --> pdb=" O LEU f2220 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N MET f2222 " --> pdb=" O ILE f2341 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE f2343 " --> pdb=" O MET f2222 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN f2299 " --> pdb=" O ARG f2340 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N MET f2342 " --> pdb=" O GLN f2299 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE f2301 " --> pdb=" O MET f2342 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU f2344 " --> pdb=" O ILE f2301 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE f2303 " --> pdb=" O GLU f2344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'f' and resid 2324 through 2326 Processing sheet with id= I, first strand: chain 'f' and resid 2537 through 2539 Processing sheet with id= J, first strand: chain 'f' and resid 2733 through 2735 removed outlier: 6.791A pdb=" N VAL f2592 " --> pdb=" O VAL f2734 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU f2591 " --> pdb=" O PHE f2708 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU f2659 " --> pdb=" O GLN f2707 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL f2709 " --> pdb=" O LEU f2659 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU f2661 " --> pdb=" O VAL f2709 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA f2711 " --> pdb=" O LEU f2661 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS f2663 " --> pdb=" O ALA f2711 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU f2616 " --> pdb=" O VAL f2660 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE f2662 " --> pdb=" O GLU f2616 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL f2618 " --> pdb=" O PHE f2662 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'f' and resid 2639 through 2643 removed outlier: 4.265A pdb=" N VAL f2648 " --> pdb=" O TRP f2700 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'f' and resid 3090 through 3093 removed outlier: 6.130A pdb=" N ILE f2990 " --> pdb=" O HIS f3063 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL f3065 " --> pdb=" O ILE f2990 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE f2992 " --> pdb=" O VAL f3065 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR f3067 " --> pdb=" O PHE f2992 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N MET f2994 " --> pdb=" O THR f3067 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER f2957 " --> pdb=" O ALA f2991 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE f2993 " --> pdb=" O SER f2957 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR f2959 " --> pdb=" O ILE f2993 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASP f2995 " --> pdb=" O TYR f2959 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'f' and resid 3697 through 3700 removed outlier: 6.807A pdb=" N LEU f3633 " --> pdb=" O PHE f3678 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N SER f3680 " --> pdb=" O LEU f3633 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL f3635 " --> pdb=" O SER f3680 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR f3610 " --> pdb=" O LEU f3634 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN f3636 " --> pdb=" O THR f3610 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR f3612 " --> pdb=" O GLN f3636 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'f' and resid 3654 through 3656 Processing sheet with id= O, first strand: chain 'f' and resid 4142 through 4147 removed outlier: 7.636A pdb=" N PHE f4145 " --> pdb=" O PRO f4040 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU f4042 " --> pdb=" O PHE f4145 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE f4147 " --> pdb=" O LEU f4042 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS f4044 " --> pdb=" O PHE f4147 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'f' and resid 4539 through 4545 Processing sheet with id= Q, first strand: chain 'f' and resid 4564 through 4566 Processing sheet with id= R, first strand: chain 'f' and resid 4568 through 4571 Processing sheet with id= S, first strand: chain 'f' and resid 4604 through 4610 removed outlier: 3.776A pdb=" N PHE f4620 " --> pdb=" O VAL f4609 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'q' and resid 268 through 271 removed outlier: 8.556A pdb=" N LEU q 228 " --> pdb=" O THR q 131 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL q 133 " --> pdb=" O LEU q 228 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL q 230 " --> pdb=" O VAL q 133 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE q 135 " --> pdb=" O VAL q 230 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR q 232 " --> pdb=" O PHE q 135 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA q 137 " --> pdb=" O THR q 232 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN q 56 " --> pdb=" O LEU q 132 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE q 134 " --> pdb=" O ASN q 56 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU q 58 " --> pdb=" O ILE q 134 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL q 136 " --> pdb=" O LEU q 58 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE q 60 " --> pdb=" O VAL q 136 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASP q 138 " --> pdb=" O PHE q 60 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS q 55 " --> pdb=" O ARG q 103 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP q 100 " --> pdb=" O ASP q 95 " (cutoff:3.500A) 1297 hydrogen bonds defined for protein. 3411 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: 12.42 Time building geometry restraints manager: 8.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.20: 1 1.20 - 1.31: 3313 1.31 - 1.43: 3358 1.43 - 1.54: 9749 1.54 - 1.65: 93 Bond restraints: 16514 Sorted by residual: bond pdb=" C PHE q 296 " pdb=" O PHE q 296 " ideal model delta sigma weight residual 1.234 1.086 0.149 1.11e-02 8.12e+03 1.80e+02 bond pdb=" N3B ANP f4705 " pdb=" PG ANP f4705 " ideal model delta sigma weight residual 1.795 1.640 0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" N3B ANP f4704 " pdb=" PG ANP f4704 " ideal model delta sigma weight residual 1.795 1.653 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" O3A ANP f4705 " pdb=" PB ANP f4705 " ideal model delta sigma weight residual 1.700 1.586 0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" O3A ANP f4704 " pdb=" PB ANP f4704 " ideal model delta sigma weight residual 1.700 1.587 0.113 2.00e-02 2.50e+03 3.21e+01 ... (remaining 16509 not shown) Histogram of bond angle deviations from ideal: 100.53 - 108.39: 741 108.39 - 116.25: 9720 116.25 - 124.11: 11769 124.11 - 131.96: 798 131.96 - 139.82: 6 Bond angle restraints: 23034 Sorted by residual: angle pdb=" CA PHE q 296 " pdb=" C PHE q 296 " pdb=" O PHE q 296 " ideal model delta sigma weight residual 120.28 110.22 10.06 1.23e+00 6.61e-01 6.69e+01 angle pdb=" N ASN q 217 " pdb=" CA ASN q 217 " pdb=" C ASN q 217 " ideal model delta sigma weight residual 110.41 101.33 9.08 1.18e+00 7.18e-01 5.92e+01 angle pdb=" CA GLY q 215 " pdb=" C GLY q 215 " pdb=" O GLY q 215 " ideal model delta sigma weight residual 121.57 115.47 6.10 8.70e-01 1.32e+00 4.92e+01 angle pdb=" N VAL f2368 " pdb=" CA VAL f2368 " pdb=" C VAL f2368 " ideal model delta sigma weight residual 112.96 106.60 6.36 1.00e+00 1.00e+00 4.04e+01 angle pdb=" PB ANP f4704 " pdb=" N3B ANP f4704 " pdb=" PG ANP f4704 " ideal model delta sigma weight residual 126.95 109.23 17.72 3.00e+00 1.11e-01 3.49e+01 ... (remaining 23029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.21: 9648 32.21 - 64.42: 39 64.42 - 96.63: 20 96.63 - 128.84: 0 128.84 - 161.05: 2 Dihedral angle restraints: 9709 sinusoidal: 110 harmonic: 9599 Sorted by residual: dihedral pdb=" O1A ANP f4705 " pdb=" O3A ANP f4705 " pdb=" PA ANP f4705 " pdb=" PB ANP f4705 " ideal model delta sinusoidal sigma weight residual 83.11 -77.94 161.05 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O1A ANP f4704 " pdb=" O3A ANP f4704 " pdb=" PA ANP f4704 " pdb=" PB ANP f4704 " ideal model delta sinusoidal sigma weight residual 83.11 -57.03 140.14 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" O1B ADP f4701 " pdb=" O3A ADP f4701 " pdb=" PB ADP f4701 " pdb=" PA ADP f4701 " ideal model delta sinusoidal sigma weight residual -60.00 -130.94 70.94 1 2.00e+01 2.50e-03 1.62e+01 ... (remaining 9706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1446 0.058 - 0.116: 1103 0.116 - 0.174: 483 0.174 - 0.232: 117 0.232 - 0.290: 14 Chirality restraints: 3163 Sorted by residual: chirality pdb=" CA VAL q 218 " pdb=" N VAL q 218 " pdb=" C VAL q 218 " pdb=" CB VAL q 218 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA MET q 185 " pdb=" N MET q 185 " pdb=" C MET q 185 " pdb=" CB MET q 185 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C3' ANP f4704 " pdb=" C2' ANP f4704 " pdb=" C4' ANP f4704 " pdb=" O3' ANP f4704 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3160 not shown) Planarity restraints: 3310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU q 277 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C GLU q 277 " -0.068 2.00e-02 2.50e+03 pdb=" O GLU q 277 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS q 278 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP q 183 " 0.018 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ASP q 183 " -0.059 2.00e-02 2.50e+03 pdb=" O ASP q 183 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR q 184 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY q 85 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C GLY q 85 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY q 85 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU q 86 " 0.019 2.00e-02 2.50e+03 ... (remaining 3307 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5808 2.82 - 3.34: 16620 3.34 - 3.86: 24956 3.86 - 4.38: 23057 4.38 - 4.90: 39796 Nonbonded interactions: 110237 Sorted by model distance: nonbonded pdb=" O1G ANP f4705 " pdb=" O2B ANP f4705 " model vdw 2.296 3.040 nonbonded pdb=" N VAL f4288 " pdb=" O LYS f4292 " model vdw 2.306 2.520 nonbonded pdb=" O ILE f3767 " pdb=" N GLU f3771 " model vdw 2.319 2.520 nonbonded pdb=" O1B ATP f4702 " pdb="MG MG f4703 " model vdw 2.375 2.170 nonbonded pdb=" O LYS f2943 " pdb=" O2A ANP f4705 " model vdw 2.425 3.040 ... (remaining 110232 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 group one per residue 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.420 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 58.380 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.012 0.155 16514 Z= 0.907 Angle : 1.298 17.718 23034 Z= 0.992 Chirality : 0.089 0.290 3163 Planarity : 0.006 0.039 3310 Dihedral : 9.683 161.048 3415 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.15), residues: 3299 helix: 1.60 (0.12), residues: 1820 sheet: -0.76 (0.29), residues: 285 loop : 0.42 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1523 time to fit residues: 28.6820 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 168 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16514 Z= 0.196 Angle : 0.461 9.907 23034 Z= 0.287 Chirality : 0.040 0.153 3163 Planarity : 0.003 0.018 3310 Dihedral : 8.060 167.763 3415 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.15), residues: 3299 helix: 2.22 (0.12), residues: 1829 sheet: -0.78 (0.28), residues: 309 loop : 0.67 (0.20), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.888 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1579 time to fit residues: 29.6754 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 249 optimal weight: 30.0000 chunk 204 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 300 optimal weight: 0.0570 chunk 324 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 297 optimal weight: 0.0470 chunk 102 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.023 16514 Z= 0.098 Angle : 0.341 6.841 23034 Z= 0.210 Chirality : 0.039 0.134 3163 Planarity : 0.002 0.015 3310 Dihedral : 7.032 178.829 3415 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.15), residues: 3299 helix: 2.89 (0.12), residues: 1825 sheet: -0.61 (0.28), residues: 300 loop : 0.88 (0.20), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1541 time to fit residues: 29.3309 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 201 optimal weight: 20.0000 chunk 301 optimal weight: 9.9990 chunk 318 optimal weight: 40.0000 chunk 157 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 16514 Z= 0.368 Angle : 0.649 14.440 23034 Z= 0.411 Chirality : 0.042 0.144 3163 Planarity : 0.004 0.021 3310 Dihedral : 8.026 175.990 3415 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3299 helix: 1.13 (0.12), residues: 1814 sheet: -1.20 (0.27), residues: 293 loop : 0.15 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.973 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1525 time to fit residues: 28.6548 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 0.0020 chunk 181 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 131 optimal weight: 0.3980 chunk 272 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 162 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 80 optimal weight: 0.0270 overall best weight: 0.8850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.020 16514 Z= 0.089 Angle : 0.350 8.037 23034 Z= 0.216 Chirality : 0.039 0.137 3163 Planarity : 0.002 0.015 3310 Dihedral : 7.166 175.541 3415 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.15), residues: 3299 helix: 2.57 (0.12), residues: 1825 sheet: -1.00 (0.29), residues: 287 loop : 0.51 (0.20), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.840 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1525 time to fit residues: 28.6191 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.5980 chunk 287 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16514 Z= 0.123 Angle : 0.356 6.932 23034 Z= 0.220 Chirality : 0.039 0.135 3163 Planarity : 0.002 0.015 3310 Dihedral : 6.846 178.378 3415 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.15), residues: 3299 helix: 2.77 (0.12), residues: 1828 sheet: -0.83 (0.30), residues: 275 loop : 0.54 (0.20), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.871 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1572 time to fit residues: 29.6019 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 180 optimal weight: 0.0030 chunk 268 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 318 optimal weight: 40.0000 chunk 199 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 overall best weight: 5.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16514 Z= 0.279 Angle : 0.508 9.835 23034 Z= 0.325 Chirality : 0.041 0.137 3163 Planarity : 0.003 0.018 3310 Dihedral : 7.414 179.757 3415 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.15), residues: 3299 helix: 1.84 (0.12), residues: 1825 sheet: -1.04 (0.30), residues: 266 loop : 0.11 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.808 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1573 time to fit residues: 29.4824 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 189 optimal weight: 0.0050 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16514 Z= 0.184 Angle : 0.400 7.186 23034 Z= 0.255 Chirality : 0.040 0.140 3163 Planarity : 0.002 0.015 3310 Dihedral : 6.934 178.017 3415 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.15), residues: 3299 helix: 2.25 (0.12), residues: 1829 sheet: -1.09 (0.30), residues: 266 loop : 0.11 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.920 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1567 time to fit residues: 29.3263 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 10.0000 chunk 304 optimal weight: 40.0000 chunk 278 optimal weight: 20.0000 chunk 296 optimal weight: 30.0000 chunk 178 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 267 optimal weight: 20.0000 chunk 280 optimal weight: 0.4980 chunk 295 optimal weight: 10.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16514 Z= 0.280 Angle : 0.512 9.995 23034 Z= 0.328 Chirality : 0.041 0.134 3163 Planarity : 0.003 0.018 3310 Dihedral : 7.376 179.506 3415 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3299 helix: 1.47 (0.12), residues: 1829 sheet: -1.38 (0.30), residues: 261 loop : -0.29 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.925 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1603 time to fit residues: 30.5002 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 148 optimal weight: 0.3980 chunk 217 optimal weight: 0.0170 chunk 328 optimal weight: 9.9990 chunk 302 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 202 optimal weight: 0.0570 chunk 160 optimal weight: 30.0000 overall best weight: 2.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16514 Z= 0.128 Angle : 0.367 7.057 23034 Z= 0.231 Chirality : 0.039 0.133 3163 Planarity : 0.002 0.014 3310 Dihedral : 6.879 176.993 3415 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.15), residues: 3299 helix: 2.39 (0.12), residues: 1826 sheet: -1.36 (0.30), residues: 263 loop : -0.06 (0.19), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6598 Ramachandran restraints generated. 3299 Oldfield, 0 Emsley, 3299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1521 time to fit residues: 28.2893 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 241 optimal weight: 0.0570 chunk 38 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 262 optimal weight: 0.0070 chunk 109 optimal weight: 2.9990 chunk 269 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 overall best weight: 2.1720 ------------------------------------------------------------------------------- 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 = 0.2603 r_free = 0.2603 target = 0.032767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2302 r_free = 0.2302 target = 0.024691 restraints weight = 276852.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2319 r_free = 0.2319 target = 0.025057 restraints weight = 210633.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.025333 restraints weight = 167770.594| |-----------------------------------------------------------------------------| r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16514 Z= 0.123 Angle : 0.351 6.585 23034 Z= 0.220 Chirality : 0.039 0.133 3163 Planarity : 0.002 0.014 3310 Dihedral : 6.610 178.560 3415 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 3299 helix: 2.81 (0.12), residues: 1820 sheet: -1.37 (0.30), residues: 265 loop : 0.03 (0.20), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP f1333 PHE 0.000 0.000 PHE f1373 TYR 0.000 0.000 TYR f1380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2296.47 seconds wall clock time: 41 minutes 44.52 seconds (2504.52 seconds total)