Starting phenix.real_space_refine on Mon Jul 22 05:42:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/07_2024/7z8l_14556_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/07_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_14556/07_2024/7z8l_14556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/07_2024/7z8l_14556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/07_2024/7z8l_14556_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8l_14556/07_2024/7z8l_14556_neut.cif" } 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-5388/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: 11.49, per 1000 atoms: 0.70 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: 7.70 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... Secondary structure from input PDB file: 158 helices and 20 sheets defined 61.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'f' and resid 1327 through 1348 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 1350 through 1354 Processing helix chain 'f' and resid 1355 through 1371 Processing helix chain 'f' and resid 1374 through 1379 removed outlier: 3.676A pdb=" N GLN f1379 " --> pdb=" O ALA f1375 " (cutoff:3.500A) Processing helix chain 'f' and resid 1380 through 1396 removed outlier: 3.501A pdb=" N GLU f1384 " --> pdb=" O TYR f1380 " (cutoff:3.500A) Processing helix chain 'f' and resid 1396 through 1404 Processing helix chain 'f' and resid 1409 through 1421 Processing helix chain 'f' and resid 1430 through 1437 removed outlier: 3.590A pdb=" N ILE f1434 " --> pdb=" O THR f1430 " (cutoff:3.500A) Processing helix chain 'f' and resid 1442 through 1473 Processing helix chain 'f' and resid 1489 through 1508 Processing helix chain 'f' and resid 1512 through 1515 removed outlier: 3.963A pdb=" N VAL f1515 " --> pdb=" O TYR f1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 1512 through 1515' Processing helix chain 'f' and resid 1516 through 1552 removed outlier: 4.269A pdb=" N VAL f1536 " --> pdb=" O ALA f1532 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP f1539 " --> pdb=" O ASP f1535 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP f1544 " --> pdb=" O VAL f1540 " (cutoff:3.500A) Processing helix chain 'f' and resid 1556 through 1561 Processing helix chain 'f' and resid 1561 through 1584 removed outlier: 3.618A pdb=" N GLU f1574 " --> pdb=" O SER f1570 " (cutoff:3.500A) Processing helix chain 'f' and resid 1587 through 1593 Processing helix chain 'f' and resid 1596 through 1626 Processing helix chain 'f' and resid 1627 through 1632 Processing helix chain 'f' and resid 1633 through 1643 Processing helix chain 'f' and resid 1646 through 1652 removed outlier: 4.025A pdb=" N LYS f1652 " --> pdb=" O LYS f1649 " (cutoff:3.500A) Processing helix chain 'f' and resid 1653 through 1658 removed outlier: 3.589A pdb=" N MET f1657 " --> pdb=" O HIS f1653 " (cutoff:3.500A) Processing helix chain 'f' and resid 1697 through 1729 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 1734 through 1745 Processing helix chain 'f' and resid 1746 through 1770 Processing helix chain 'f' and resid 1775 through 1798 removed outlier: 3.536A pdb=" N LEU f1797 " --> pdb=" O ALA f1793 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET f1798 " --> pdb=" O ASP f1794 " (cutoff:3.500A) Processing helix chain 'f' and resid 1801 through 1829 removed outlier: 3.635A pdb=" N HIS f1817 " --> pdb=" O THR f1813 " (cutoff:3.500A) Processing helix chain 'f' and resid 1835 through 1840 Processing helix chain 'f' and resid 1882 through 1898 Processing helix chain 'f' and resid 1911 through 1923 Processing helix chain 'f' and resid 1937 through 1939 No H-bonds generated for 'chain 'f' and resid 1937 through 1939' Processing helix chain 'f' and resid 1940 through 1952 Processing helix chain 'f' and resid 1959 through 1963 Processing helix chain 'f' and resid 1964 through 1984 Processing helix chain 'f' and resid 2045 through 2057 Processing helix chain 'f' and resid 2062 through 2080 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 2089 through 2118 Processing helix chain 'f' and resid 2123 through 2130 removed outlier: 3.711A pdb=" N ASN f2130 " --> pdb=" O GLU f2126 " (cutoff:3.500A) Processing helix chain 'f' and resid 2132 through 2146 Processing helix chain 'f' and resid 2147 through 2149 No H-bonds generated for 'chain 'f' and resid 2147 through 2149' Processing helix chain 'f' and resid 2153 through 2165 Processing helix chain 'f' and resid 2175 through 2189 Processing helix chain 'f' and resid 2200 through 2217 Processing helix chain 'f' and resid 2229 through 2246 removed outlier: 3.726A pdb=" N ARG f2243 " --> pdb=" O LYS f2239 " (cutoff:3.500A) Processing helix chain 'f' and resid 2260 through 2266 Processing helix chain 'f' and resid 2278 through 2290 Processing helix chain 'f' and resid 2309 through 2311 No H-bonds generated for 'chain 'f' and resid 2309 through 2311' Processing helix chain 'f' and resid 2312 through 2320 removed outlier: 4.255A pdb=" N SER f2317 " --> pdb=" O GLU f2313 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL f2318 " --> pdb=" O ASN f2314 " (cutoff:3.500A) Processing helix chain 'f' and resid 2352 through 2359 removed outlier: 3.564A pdb=" N ARG f2358 " --> pdb=" O ALA f2354 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS f2359 " --> pdb=" O THR f2355 " (cutoff:3.500A) Processing helix chain 'f' and resid 2365 through 2369 removed outlier: 3.639A pdb=" N LEU f2369 " --> pdb=" O GLU f2366 " (cutoff:3.500A) Processing helix chain 'f' and resid 2370 through 2385 removed outlier: 3.601A pdb=" N SER f2384 " --> pdb=" O ALA f2380 " (cutoff:3.500A) Processing helix chain 'f' and resid 2395 through 2400 removed outlier: 3.540A pdb=" N LYS f2399 " --> pdb=" O GLN f2395 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY f2400 " --> pdb=" O ARG f2396 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 2395 through 2400' Processing helix chain 'f' and resid 2410 through 2424 Processing helix chain 'f' and resid 2425 through 2428 removed outlier: 3.977A pdb=" N THR f2428 " --> pdb=" O PRO f2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 2425 through 2428' Processing helix chain 'f' and resid 2431 through 2443 removed outlier: 3.658A pdb=" N GLN f2442 " --> pdb=" O GLU f2438 " (cutoff:3.500A) Processing helix chain 'f' and resid 2450 through 2476 Processing helix chain 'f' and resid 2482 through 2503 removed outlier: 3.562A pdb=" N VAL f2495 " --> pdb=" O GLN f2491 " (cutoff:3.500A) Processing helix chain 'f' and resid 2504 through 2506 No H-bonds generated for 'chain 'f' and resid 2504 through 2506' Processing helix chain 'f' and resid 2507 through 2522 Processing helix chain 'f' and resid 2533 through 2535 No H-bonds generated for 'chain 'f' and resid 2533 through 2535' Processing helix chain 'f' and resid 2549 through 2552 removed outlier: 3.654A pdb=" N VAL f2552 " --> pdb=" O GLN f2549 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 2549 through 2552' Processing helix chain 'f' and resid 2571 through 2587 removed outlier: 4.017A pdb=" N GLU f2587 " --> pdb=" O THR f2583 " (cutoff:3.500A) Processing helix chain 'f' and resid 2600 through 2612 removed outlier: 3.586A pdb=" N LEU f2612 " --> pdb=" O ALA f2608 " (cutoff:3.500A) Processing helix chain 'f' and resid 2627 through 2638 removed outlier: 4.096A pdb=" N LEU f2631 " --> pdb=" O THR f2627 " (cutoff:3.500A) Processing helix chain 'f' and resid 2677 through 2690 Processing helix chain 'f' and resid 2724 through 2729 Processing helix chain 'f' and resid 2739 through 2756 removed outlier: 4.324A pdb=" N SER f2743 " --> pdb=" O PRO f2739 " (cutoff:3.500A) Processing helix chain 'f' and resid 2757 through 2759 No H-bonds generated for 'chain 'f' and resid 2757 through 2759' Processing helix chain 'f' and resid 2762 through 2764 No H-bonds generated for 'chain 'f' and resid 2762 through 2764' Processing helix chain 'f' and resid 2765 through 2784 removed outlier: 3.580A pdb=" N TYR f2777 " --> pdb=" O MET f2773 " (cutoff:3.500A) Processing helix chain 'f' and resid 2795 through 2811 removed outlier: 3.789A pdb=" N MET f2799 " --> pdb=" O SER f2795 " (cutoff:3.500A) Processing helix chain 'f' and resid 2817 through 2834 Processing helix chain 'f' and resid 2839 through 2858 removed outlier: 3.604A pdb=" N ASP f2851 " --> pdb=" O ASP f2847 " (cutoff:3.500A) Processing helix chain 'f' and resid 2862 through 2867 Processing helix chain 'f' and resid 2885 through 2902 removed outlier: 3.983A pdb=" N GLU f2902 " --> pdb=" O LYS f2898 " (cutoff:3.500A) Processing helix chain 'f' and resid 2912 through 2928 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 2945 through 2954 Processing helix chain 'f' and resid 2968 through 2985 removed outlier: 3.505A pdb=" N PHE f2972 " --> pdb=" O THR f2968 " (cutoff:3.500A) 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 3006 through 3015 removed outlier: 4.164A pdb=" N THR f3010 " --> pdb=" O GLU f3006 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU f3011 " --> pdb=" O ARG f3007 " (cutoff:3.500A) Processing helix chain 'f' and resid 3023 through 3041 removed outlier: 3.718A pdb=" N ALA f3027 " --> pdb=" O GLY f3023 " (cutoff:3.500A) Processing helix chain 'f' and resid 3046 through 3061 Processing helix chain 'f' and resid 3082 through 3089 Processing helix chain 'f' and resid 3098 through 3108 Processing helix chain 'f' and resid 3138 through 3164 removed outlier: 3.699A pdb=" N HIS f3151 " --> pdb=" O CYS f3147 " (cutoff:3.500A) Processing helix chain 'f' and resid 3172 through 3220 removed outlier: 3.767A pdb=" N TYR f3176 " --> pdb=" O THR f3172 " (cutoff:3.500A) Processing helix chain 'f' and resid 3471 through 3516 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 3521 through 3539 Processing helix chain 'f' and resid 3548 through 3553 Processing helix chain 'f' and resid 3555 through 3565 Processing helix chain 'f' and resid 3570 through 3580 Processing helix chain 'f' and resid 3594 through 3604 removed outlier: 3.757A pdb=" N GLU f3598 " --> pdb=" O GLY f3594 " (cutoff:3.500A) Processing helix chain 'f' and resid 3605 through 3608 Processing helix chain 'f' and resid 3616 through 3618 No H-bonds generated for 'chain 'f' and resid 3616 through 3618' Processing helix chain 'f' and resid 3619 through 3630 Processing helix chain 'f' and resid 3637 through 3641 removed outlier: 3.687A pdb=" N SER f3640 " --> pdb=" O ASP f3637 " (cutoff:3.500A) Processing helix chain 'f' and resid 3642 through 3644 No H-bonds generated for 'chain 'f' and resid 3642 through 3644' Processing helix chain 'f' and resid 3645 through 3651 Processing helix chain 'f' and resid 3689 through 3695 removed outlier: 3.519A pdb=" N SER f3694 " --> pdb=" O PRO f3690 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG f3695 " --> pdb=" O ASP f3691 " (cutoff:3.500A) Processing helix chain 'f' and resid 3704 through 3721 Processing helix chain 'f' and resid 3721 through 3730 Processing helix chain 'f' and resid 3735 through 3752 removed outlier: 4.190A pdb=" N GLN f3739 " --> pdb=" O GLN f3735 " (cutoff:3.500A) Processing helix chain 'f' and resid 3766 through 3786 removed outlier: 3.869A pdb=" N LEU f3773 " --> pdb=" O THR f3769 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU f3776 " --> pdb=" O ASN f3772 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA f3778 " --> pdb=" O LYS f3774 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL f3784 " --> pdb=" O VAL f3780 " (cutoff:3.500A) Processing helix chain 'f' and resid 3788 through 3801 removed outlier: 3.597A pdb=" N GLN f3800 " --> pdb=" O THR f3796 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR f3801 " --> pdb=" O VAL f3797 " (cutoff:3.500A) Processing helix chain 'f' and resid 3801 through 3818 removed outlier: 3.593A pdb=" N SER f3805 " --> pdb=" O TYR f3801 " (cutoff:3.500A) Processing helix chain 'f' and resid 3819 through 3821 No H-bonds generated for 'chain 'f' and resid 3819 through 3821' Processing helix chain 'f' and resid 3828 through 3841 removed outlier: 3.630A pdb=" N PHE f3832 " --> pdb=" O SER f3828 " (cutoff:3.500A) Processing helix chain 'f' and resid 3843 through 3847 Processing helix chain 'f' and resid 3851 through 3873 Processing helix chain 'f' and resid 3874 through 3875 No H-bonds generated for 'chain 'f' and resid 3874 through 3875' Processing helix chain 'f' and resid 3876 through 3878 No H-bonds generated for 'chain 'f' and resid 3876 through 3878' Processing helix chain 'f' and resid 3879 through 3895 Processing helix chain 'f' and resid 3901 through 3911 Processing helix chain 'f' and resid 3928 through 3939 Processing helix chain 'f' and resid 3946 through 3954 Processing helix chain 'f' and resid 3956 through 3962 removed outlier: 3.597A pdb=" N TRP f3960 " --> pdb=" O GLN f3956 " (cutoff:3.500A) Processing helix chain 'f' and resid 3965 through 3970 removed outlier: 3.502A pdb=" N GLN f3968 " --> pdb=" O SER f3965 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL f3970 " --> pdb=" O GLU f3967 " (cutoff:3.500A) Processing helix chain 'f' and resid 3981 through 3997 Processing helix chain 'f' and resid 4000 through 4013 Processing helix chain 'f' and resid 4026 through 4034 removed outlier: 3.717A pdb=" N ILE f4030 " --> pdb=" O ASP f4026 " (cutoff:3.500A) Processing helix chain 'f' and resid 4051 through 4063 removed outlier: 3.775A pdb=" N VAL f4055 " --> pdb=" O ALA f4051 " (cutoff:3.500A) Processing helix chain 'f' and resid 4073 through 4091 removed outlier: 3.617A pdb=" N PHE f4077 " --> pdb=" O SER f4073 " (cutoff:3.500A) 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 4102 through 4114 Processing helix chain 'f' and resid 4135 through 4141 Processing helix chain 'f' and resid 4152 through 4164 Processing helix chain 'f' and resid 4165 through 4171 removed outlier: 3.576A pdb=" N ILE f4169 " --> pdb=" O PRO f4165 " (cutoff:3.500A) Processing helix chain 'f' and resid 4175 through 4194 Processing helix chain 'f' and resid 4195 through 4197 No H-bonds generated for 'chain 'f' and resid 4195 through 4197' Processing helix chain 'f' and resid 4208 through 4228 removed outlier: 3.608A pdb=" N LEU f4212 " --> pdb=" O GLY f4208 " (cutoff:3.500A) Processing helix chain 'f' and resid 4239 through 4250 Processing helix chain 'f' and resid 4258 through 4273 Processing helix chain 'f' and resid 4274 through 4279 Processing helix chain 'f' and resid 4289 through 4291 No H-bonds generated for 'chain 'f' and resid 4289 through 4291' Processing helix chain 'f' and resid 4301 through 4311 removed outlier: 3.516A pdb=" N PHE f4305 " --> pdb=" O ARG f4301 " (cutoff:3.500A) Processing helix chain 'f' and resid 4317 through 4321 Processing helix chain 'f' and resid 4325 through 4345 removed outlier: 3.909A pdb=" N ARG f4329 " --> pdb=" O ASN f4325 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR f4333 " --> pdb=" O ARG f4329 " (cutoff:3.500A) Processing helix chain 'f' and resid 4376 through 4391 removed outlier: 3.737A pdb=" N THR f4382 " --> pdb=" O ARG f4378 " (cutoff:3.500A) Processing helix chain 'f' and resid 4401 through 4406 removed outlier: 4.212A pdb=" N LYS f4406 " --> pdb=" O VAL f4402 " (cutoff:3.500A) Processing helix chain 'f' and resid 4407 through 4439 Processing helix chain 'f' and resid 4445 through 4458 Processing helix chain 'f' and resid 4461 through 4465 Processing helix chain 'f' and resid 4474 through 4500 removed outlier: 3.623A pdb=" N TRP f4478 " --> pdb=" O THR f4474 " (cutoff:3.500A) Processing helix chain 'f' and resid 4502 through 4507 removed outlier: 4.333A pdb=" N ASN f4506 " --> pdb=" O LYS f4502 " (cutoff:3.500A) Processing helix chain 'f' and resid 4512 through 4514 No H-bonds generated for 'chain 'f' and resid 4512 through 4514' Processing helix chain 'f' and resid 4516 through 4533 removed outlier: 3.653A pdb=" N TYR f4520 " --> pdb=" O VAL f4516 " (cutoff:3.500A) Processing helix chain 'f' and resid 4631 through 4638 removed outlier: 3.964A pdb=" N PHE f4635 " --> pdb=" O ASP f4631 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 75 Processing helix chain 'q' and resid 112 through 122 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 127 through 129 No H-bonds generated for 'chain 'q' and resid 127 through 129' Processing helix chain 'q' and resid 141 through 143 No H-bonds generated for 'chain 'q' and resid 141 through 143' Processing helix chain 'q' and resid 144 through 163 removed outlier: 3.559A pdb=" N LYS q 162 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Processing helix chain 'q' and resid 166 through 183 Processing helix chain 'q' and resid 233 through 235 No H-bonds generated for 'chain 'q' and resid 233 through 235' Processing helix chain 'q' and resid 236 through 244 removed outlier: 4.308A pdb=" N LYS q 242 " --> pdb=" O SER q 238 " (cutoff:3.500A) Processing helix chain 'q' and resid 247 through 266 Processing helix chain 'q' and resid 279 through 293 Processing helix chain 'q' and resid 316 through 322 removed outlier: 3.734A pdb=" N ILE q 322 " --> pdb=" O LYS q 318 " (cutoff:3.500A) Processing helix chain 'q' and resid 323 through 327 Processing helix chain 'q' and resid 335 through 340 removed outlier: 3.620A pdb=" N PHE q 339 " --> pdb=" O ALA q 335 " (cutoff:3.500A) Processing sheet with id=AA1, 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=AA2, first strand: chain 'f' and resid 1663 through 1666 removed outlier: 6.870A pdb=" N SER f1663 " --> pdb=" O ILE f1676 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE f1676 " --> pdb=" O SER f1663 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE f1665 " --> pdb=" O LEU f1674 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLY f1675 " --> pdb=" O THR f1688 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N THR f1688 " --> pdb=" O GLY f1675 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N SER f1677 " --> pdb=" O PHE f1686 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N PHE f1686 " --> pdb=" O SER f1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'f' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'f' and resid 1901 through 1905 removed outlier: 6.455A pdb=" N GLY f1901 " --> pdb=" O ARG f2037 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU f2039 " --> pdb=" O GLY f1901 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER f1903 " --> pdb=" O LEU f2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'f' and resid 1927 through 1931 removed outlier: 6.138A pdb=" N GLY f1955 " --> pdb=" O PHE f2015 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'f' and resid 2249 through 2254 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) removed outlier: 7.001A pdb=" N GLY f2219 " --> pdb=" O GLY f2360 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N VAL f2362 " --> pdb=" O GLY f2219 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET f2221 " --> pdb=" O VAL f2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'f' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'f' and resid 2616 through 2620 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) 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: 6.476A pdb=" N LEU f2591 " --> pdb=" O GLY f2710 " (cutoff:3.500A) Processing sheet with id=AB2, 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=AB3, first strand: chain 'f' and resid 2873 through 2874 removed outlier: 3.552A pdb=" N SER f2874 " --> pdb=" O ILE f2882 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE f2882 " --> pdb=" O SER f2874 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'f' and resid 2957 through 2960 Processing sheet with id=AB5, first strand: chain 'f' and resid 3610 through 3613 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) removed outlier: 6.044A pdb=" N LEU f3588 " --> pdb=" O VAL f3699 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 3654 through 3656 Processing sheet with id=AB7, first strand: chain 'f' and resid 4066 through 4070 removed outlier: 6.343A pdb=" N THR f4067 " --> pdb=" O MET f4095 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS f4097 " --> pdb=" O THR f4067 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE f4069 " --> pdb=" O LYS f4097 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL f4094 " --> pdb=" O PHE f4125 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR f4127 " --> pdb=" O VAL f4094 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU f4096 " --> pdb=" O THR f4127 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLU f4129 " --> pdb=" O LEU f4096 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL f4041 " --> pdb=" O LEU f4126 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET f4128 " --> pdb=" O VAL f4041 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N MET f4043 " --> pdb=" O MET f4128 " (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) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'f' and resid 4283 through 4288 removed outlier: 5.753A pdb=" N CYS f4286 " --> pdb=" O ILE f4294 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE f4294 " --> pdb=" O CYS f4286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'f' and resid 4509 through 4510 removed outlier: 3.537A pdb=" N THR f4561 " --> pdb=" O VAL f4509 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'f' and resid 4568 through 4571 removed outlier: 3.776A pdb=" N PHE f4620 " --> pdb=" O VAL f4609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'q' and resid 86 through 95 removed outlier: 3.500A pdb=" N ASP q 100 " --> pdb=" O ASP q 95 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS q 55 " --> pdb=" O ASN q 105 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N TRP q 107 " --> pdb=" O LYS q 55 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE q 57 " --> pdb=" O TRP q 107 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU q 109 " --> pdb=" O ILE q 57 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL q 59 " --> pdb=" O LEU q 109 " (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: 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) 1474 hydrogen bonds defined for protein. 4281 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: 12.90 Time building geometry restraints manager: 8.45 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: 5726 2.82 - 3.34: 16529 3.34 - 3.86: 24889 3.86 - 4.38: 22642 4.38 - 4.90: 39743 Nonbonded interactions: 109529 Sorted by model distance: nonbonded pdb=" O1G ANP f4705 " pdb=" O2B ANP f4705 " model vdw 2.296 3.040 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 nonbonded pdb=" N GLY f1909 " pdb=" O1B ADP f4701 " model vdw 2.495 2.520 nonbonded pdb=" O2' ATP f4702 " pdb=" O3' ATP f4702 " model vdw 2.505 2.432 ... (remaining 109524 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 62.330 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.400 ------------------------------------------------------------------------------- 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= 0.900 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 : 1.799 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1736 time to fit residues: 32.8740 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.779 ------------------------------------------------------------------------------- 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: 7.9990 chunk 250 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 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: 3.7388 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16514 Z= 0.232 Angle : 0.495 11.262 23034 Z= 0.308 Chirality : 0.041 0.169 3163 Planarity : 0.003 0.014 3310 Dihedral : 8.197 167.412 3415 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 2.10 (0.15), residues: 3299 helix: 2.32 (0.12), residues: 1845 sheet: -0.83 (0.27), residues: 317 loop : 0.63 (0.20), residues: 1137 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 : 1.885 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1515 time to fit residues: 28.9097 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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: 20.0000 chunk 93 optimal weight: 0.7980 chunk 249 optimal weight: 30.0000 chunk 204 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 300 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 240 optimal weight: 0.0370 overall best weight: 2.1664 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16514 Z= 0.125 Angle : 0.357 8.742 23034 Z= 0.220 Chirality : 0.039 0.138 3163 Planarity : 0.002 0.011 3310 Dihedral : 6.972 174.066 3415 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 3.03 (0.15), residues: 3299 helix: 3.25 (0.12), residues: 1856 sheet: -0.72 (0.28), residues: 294 loop : 0.74 (0.20), residues: 1149 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 : 1.762 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1504 time to fit residues: 28.1107 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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: 30.0000 chunk 225 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 chunk 301 optimal weight: 10.0000 chunk 318 optimal weight: 40.0000 chunk 157 optimal weight: 9.9990 chunk 285 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16514 Z= 0.362 Angle : 0.630 13.848 23034 Z= 0.402 Chirality : 0.042 0.141 3163 Planarity : 0.004 0.015 3310 Dihedral : 7.972 176.910 3415 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.39 % 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: 0.99 (0.15), residues: 3299 helix: 1.45 (0.12), residues: 1874 sheet: -1.39 (0.27), residues: 306 loop : 0.07 (0.20), residues: 1119 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 : 1.771 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1532 time to fit residues: 29.0905 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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: 0.0040 chunk 181 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 162 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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: 0.7900 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.019 16514 Z= 0.083 Angle : 0.343 7.272 23034 Z= 0.212 Chirality : 0.039 0.138 3163 Planarity : 0.002 0.008 3310 Dihedral : 6.992 172.731 3415 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 2.78 (0.15), residues: 3299 helix: 3.14 (0.12), residues: 1882 sheet: -1.09 (0.29), residues: 289 loop : 0.44 (0.20), residues: 1128 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 : 1.750 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1554 time to fit residues: 28.7331 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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: 0.8980 chunk 287 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 319 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 147 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 0.0570 chunk 167 optimal weight: 9.9990 overall best weight: 2.3902 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16514 Z= 0.133 Angle : 0.363 6.464 23034 Z= 0.224 Chirality : 0.039 0.137 3163 Planarity : 0.002 0.011 3310 Dihedral : 6.859 178.985 3415 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: 2.87 (0.16), residues: 3299 helix: 3.21 (0.12), residues: 1890 sheet: -1.04 (0.29), residues: 290 loop : 0.46 (0.21), residues: 1119 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 : 1.844 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1577 time to fit residues: 29.9479 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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: 0.9980 chunk 35 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 318 optimal weight: 40.0000 chunk 199 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16514 Z= 0.156 Angle : 0.378 6.389 23034 Z= 0.238 Chirality : 0.039 0.137 3163 Planarity : 0.002 0.011 3310 Dihedral : 6.859 177.810 3415 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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 (0.16), residues: 3299 helix: 3.15 (0.12), residues: 1887 sheet: -1.02 (0.30), residues: 283 loop : 0.30 (0.20), residues: 1129 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 : 1.949 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1633 time to fit residues: 30.2028 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.994 ------------------------------------------------------------------------------- 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: 7.9990 chunk 127 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16514 Z= 0.330 Angle : 0.556 10.637 23034 Z= 0.360 Chirality : 0.041 0.135 3163 Planarity : 0.003 0.015 3310 Dihedral : 7.376 179.869 3415 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % 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: 1.24 (0.15), residues: 3299 helix: 1.82 (0.12), residues: 1874 sheet: -1.21 (0.31), residues: 267 loop : -0.25 (0.19), residues: 1158 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 : 1.762 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1537 time to fit residues: 28.7320 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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: 9.9990 chunk 304 optimal weight: 30.0000 chunk 278 optimal weight: 9.9990 chunk 296 optimal weight: 30.0000 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 232 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16514 Z= 0.384 Angle : 0.619 12.032 23034 Z= 0.405 Chirality : 0.042 0.161 3163 Planarity : 0.004 0.018 3310 Dihedral : 7.870 176.497 3415 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % 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: -0.23 (0.15), residues: 3299 helix: 0.63 (0.12), residues: 1867 sheet: -1.59 (0.32), residues: 243 loop : -0.97 (0.19), residues: 1189 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 : 1.867 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1597 time to fit residues: 29.9143 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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: 10.0000 chunk 313 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 217 optimal weight: 0.8980 chunk 328 optimal weight: 9.9990 chunk 302 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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: 0.8046 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16514 Z= 0.286 Angle : 0.509 8.676 23034 Z= 0.329 Chirality : 0.041 0.137 3163 Planarity : 0.003 0.016 3310 Dihedral : 7.434 176.926 3415 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % 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: 0.18 (0.15), residues: 3299 helix: 1.10 (0.12), residues: 1876 sheet: -1.64 (0.33), residues: 241 loop : -1.00 (0.19), residues: 1182 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 : 1.832 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1566 time to fit residues: 29.1994 Evaluate side-chains 90 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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: 9.9990 chunk 278 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 262 optimal weight: 0.0060 chunk 109 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.2622 r_free = 0.2622 target = 0.033069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2331 r_free = 0.2331 target = 0.025365 restraints weight = 231898.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.025714 restraints weight = 171938.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.025906 restraints weight = 137591.800| |-----------------------------------------------------------------------------| r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.019 16514 Z= 0.079 Angle : 0.343 7.085 23034 Z= 0.211 Chirality : 0.039 0.134 3163 Planarity : 0.002 0.008 3310 Dihedral : 6.652 172.907 3415 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: 2.03 (0.15), residues: 3299 helix: 2.82 (0.12), residues: 1891 sheet: -1.54 (0.31), residues: 257 loop : -0.52 (0.20), residues: 1151 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: 2298.61 seconds wall clock time: 41 minutes 15.10 seconds (2475.10 seconds total)