Starting phenix.real_space_refine on Wed Feb 21 01:54:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi6_23841/02_2024/7mi6_23841_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi6_23841/02_2024/7mi6_23841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi6_23841/02_2024/7mi6_23841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi6_23841/02_2024/7mi6_23841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi6_23841/02_2024/7mi6_23841_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi6_23841/02_2024/7mi6_23841_updated.pdb" } resolution = 3.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9873 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Br 2 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 91 5.16 5 Cl 2 4.86 5 C 12620 2.51 5 N 3247 2.21 5 O 3687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1384": "OE1" <-> "OE2" Residue "A TYR 1420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1536": "NH1" <-> "NH2" Residue "A PHE 1537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1543": "OD1" <-> "OD2" Residue "A ASP 1544": "OD1" <-> "OD2" Residue "A GLU 1594": "OE1" <-> "OE2" Residue "A ASP 1600": "OD1" <-> "OD2" Residue "A ASP 1612": "OD1" <-> "OD2" Residue "A GLU 1614": "OE1" <-> "OE2" Residue "A ASP 1677": "OD1" <-> "OD2" Residue "A ASP 1685": "OD1" <-> "OD2" Residue "A ASP 1692": "OD1" <-> "OD2" Residue "A PHE 1734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1824": "OD1" <-> "OD2" Residue "A ASP 1827": "OD1" <-> "OD2" Residue "A GLU 1855": "OE1" <-> "OE2" Residue "A GLU 1883": "OE1" <-> "OE2" Residue "A GLU 1884": "OE1" <-> "OE2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A GLU 1931": "OE1" <-> "OE2" Residue "A PHE 1939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2112": "OE1" <-> "OE2" Residue "A GLU 2124": "OE1" <-> "OE2" Residue "A TYR 2298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2520": "OE1" <-> "OE2" Residue "A ARG 2528": "NH1" <-> "NH2" Residue "A ARG 2552": "NH1" <-> "NH2" Residue "A TYR 2650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2939": "OE1" <-> "OE2" Residue "A GLU 2947": "OE1" <-> "OE2" Residue "A ARG 2974": "NH1" <-> "NH2" Residue "A ARG 2997": "NH1" <-> "NH2" Residue "A ARG 3305": "NH1" <-> "NH2" Residue "A PHE 3313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3365": "NH1" <-> "NH2" Residue "A TYR 3389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3434": "OE1" <-> "OE2" Residue "A ARG 3445": "NH1" <-> "NH2" Residue "A PHE 3457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3464": "NH1" <-> "NH2" Residue "A GLU 3469": "OE1" <-> "OE2" Residue "A PHE 3470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3545": "NH1" <-> "NH2" Residue "A GLU 3563": "OE1" <-> "OE2" Residue "A GLU 3606": "OE1" <-> "OE2" Residue "A PHE 3638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3672": "OD1" <-> "OD2" Residue "A TYR 3679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3717": "OE1" <-> "OE2" Residue "A GLU 3728": "OE1" <-> "OE2" Residue "A ASP 3731": "OD1" <-> "OD2" Residue "A ASP 3739": "OD1" <-> "OD2" Residue "A ASP 3742": "OD1" <-> "OD2" Residue "A TYR 3746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3770": "OD1" <-> "OD2" Residue "A GLU 3771": "OE1" <-> "OE2" Residue "A GLU 3791": "OE1" <-> "OE2" Residue "A ARG 3792": "NH1" <-> "NH2" Residue "A GLU 3802": "OE1" <-> "OE2" Residue "A TYR 3854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3860": "OE1" <-> "OE2" Residue "A GLU 3898": "OE1" <-> "OE2" Residue "A ASP 3905": "OD1" <-> "OD2" Residue "A ASP 3909": "OD1" <-> "OD2" Residue "A PHE 3916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4000": "OE1" <-> "OE2" Residue "A GLU 4005": "OE1" <-> "OE2" Residue "A ASP 4019": "OD1" <-> "OD2" Residue "A ARG 4028": "NH1" <-> "NH2" Residue "A GLU 4041": "OE1" <-> "OE2" Residue "A GLU 4054": "OE1" <-> "OE2" Residue "A GLU 4068": "OE1" <-> "OE2" Residue "A GLU 4074": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19653 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 19653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2423, 19653 Unusual residues: {' MG': 1, 'ATP': 1, 'ZG7': 2} Classifications: {'peptide': 2419, 'undetermined': 4} Link IDs: {'PTRANS': 66, 'TRANS': 2352, None: 4} Not linked: pdbres="MET A4092 " pdbres="ZG7 A4201 " Not linked: pdbres="ZG7 A4201 " pdbres="ZG7 A4202 " Not linked: pdbres="ZG7 A4202 " pdbres="ATP A4203 " Not linked: pdbres="ATP A4203 " pdbres=" MG A4204 " Chain breaks: 3 Time building chain proxies: 10.13, per 1000 atoms: 0.52 Number of scatterers: 19653 At special positions: 0 Unit cell: (118.622, 155.4, 154.364, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Br 2 34.99 Cl 2 17.00 S 91 16.00 P 3 15.00 Mg 1 11.99 O 3687 8.00 N 3247 7.00 C 12620 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: 7.76 Conformation dependent library (CDL) restraints added in 3.2 seconds 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 14 sheets defined 57.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... Processing helix chain 'A' and resid 1366 through 1380 removed outlier: 3.528A pdb=" N ARG A1373 " --> pdb=" O LYS A1369 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1380 " --> pdb=" O LYS A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1417 removed outlier: 4.170A pdb=" N LYS A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA A1417 " --> pdb=" O VAL A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1459 removed outlier: 3.760A pdb=" N LYS A1437 " --> pdb=" O SER A1433 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A1444 " --> pdb=" O GLU A1440 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A1458 " --> pdb=" O ASP A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1470 through 1493 removed outlier: 3.740A pdb=" N SER A1478 " --> pdb=" O SER A1474 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A1493 " --> pdb=" O ARG A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1501 Processing helix chain 'A' and resid 1506 through 1533 removed outlier: 3.605A pdb=" N SER A1524 " --> pdb=" O LYS A1520 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A1525 " --> pdb=" O SER A1521 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A1526 " --> pdb=" O SER A1522 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU A1527 " --> pdb=" O LEU A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1540 Processing helix chain 'A' and resid 1542 through 1552 Processing helix chain 'A' and resid 1557 through 1566 removed outlier: 3.536A pdb=" N LYS A1560 " --> pdb=" O GLN A1557 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A1563 " --> pdb=" O LYS A1560 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A1565 " --> pdb=" O MET A1562 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A1566 " --> pdb=" O LYS A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1631 removed outlier: 3.787A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1640 Processing helix chain 'A' and resid 1645 through 1666 removed outlier: 3.749A pdb=" N LYS A1662 " --> pdb=" O GLU A1658 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A1665 " --> pdb=" O GLU A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1688 removed outlier: 3.522A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1716 removed outlier: 3.973A pdb=" N LYS A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS A1697 " --> pdb=" O ASN A1693 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1730 removed outlier: 3.904A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1745 No H-bonds generated for 'chain 'A' and resid 1743 through 1745' Processing helix chain 'A' and resid 1773 through 1787 Processing helix chain 'A' and resid 1802 through 1812 Processing helix chain 'A' and resid 1829 through 1841 Processing helix chain 'A' and resid 1855 through 1874 Processing helix chain 'A' and resid 1910 through 1913 No H-bonds generated for 'chain 'A' and resid 1910 through 1913' Processing helix chain 'A' and resid 1927 through 1937 Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1970 through 1984 Proline residue: A1982 - end of helix Processing helix chain 'A' and resid 1991 through 2005 removed outlier: 4.000A pdb=" N LEU A2003 " --> pdb=" O LYS A1999 " (cutoff:3.500A) Proline residue: A2004 - end of helix Processing helix chain 'A' and resid 2008 through 2021 removed outlier: 4.052A pdb=" N LEU A2012 " --> pdb=" O ASP A2008 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A2013 " --> pdb=" O THR A2009 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2045 Processing helix chain 'A' and resid 2051 through 2065 removed outlier: 3.945A pdb=" N LYS A2065 " --> pdb=" O TYR A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2095 Processing helix chain 'A' and resid 2106 through 2108 No H-bonds generated for 'chain 'A' and resid 2106 through 2108' Processing helix chain 'A' and resid 2111 through 2114 No H-bonds generated for 'chain 'A' and resid 2111 through 2114' Processing helix chain 'A' and resid 2129 through 2139 Processing helix chain 'A' and resid 2160 through 2170 removed outlier: 3.570A pdb=" N MET A2166 " --> pdb=" O TYR A2162 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER A2168 " --> pdb=" O GLU A2164 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL A2169 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A2170 " --> pdb=" O MET A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2209 removed outlier: 3.792A pdb=" N ARG A2209 " --> pdb=" O ALA A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2222 through 2240 removed outlier: 3.834A pdb=" N ALA A2236 " --> pdb=" O LYS A2232 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN A2239 " --> pdb=" O GLU A2235 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS A2240 " --> pdb=" O ALA A2236 " (cutoff:3.500A) Processing helix chain 'A' and resid 2243 through 2257 removed outlier: 4.187A pdb=" N LYS A2248 " --> pdb=" O PHE A2244 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2267 Processing helix chain 'A' and resid 2280 through 2282 No H-bonds generated for 'chain 'A' and resid 2280 through 2282' Processing helix chain 'A' and resid 2284 through 2304 removed outlier: 3.735A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A2299 " --> pdb=" O ILE A2295 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLN A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TRP A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A2303 " --> pdb=" O ARG A2299 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASN A2304 " --> pdb=" O GLN A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2327 Processing helix chain 'A' and resid 2333 through 2345 removed outlier: 3.788A pdb=" N GLN A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A2341 " --> pdb=" O ALA A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2382 through 2386 Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2424 through 2434 removed outlier: 3.890A pdb=" N MET A2428 " --> pdb=" O LYS A2424 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2451 through 2461 removed outlier: 4.069A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N HIS A2461 " --> pdb=" O ALA A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2512 Processing helix chain 'A' and resid 2548 through 2553 removed outlier: 4.596A pdb=" N HIS A2553 " --> pdb=" O ARG A2549 " (cutoff:3.500A) Processing helix chain 'A' and resid 2565 through 2581 removed outlier: 4.568A pdb=" N LEU A2581 " --> pdb=" O ALA A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2606 removed outlier: 4.658A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A2590 " --> pdb=" O SER A2587 " (cutoff:3.500A) Proline residue: A2591 - end of helix removed outlier: 3.659A pdb=" N LEU A2599 " --> pdb=" O SER A2596 " (cutoff:3.500A) Processing helix chain 'A' and resid 2619 through 2634 removed outlier: 3.865A pdb=" N ARG A2624 " --> pdb=" O GLU A2621 " (cutoff:3.500A) Processing helix chain 'A' and resid 2641 through 2659 removed outlier: 4.967A pdb=" N ASP A2658 " --> pdb=" O ARG A2654 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ARG A2659 " --> pdb=" O ILE A2655 " (cutoff:3.500A) Processing helix chain 'A' and resid 2663 through 2680 Processing helix chain 'A' and resid 2709 through 2726 Processing helix chain 'A' and resid 2736 through 2750 Processing helix chain 'A' and resid 2766 through 2777 removed outlier: 3.594A pdb=" N ARG A2771 " --> pdb=" O THR A2767 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2808 Processing helix chain 'A' and resid 2819 through 2821 No H-bonds generated for 'chain 'A' and resid 2819 through 2821' Processing helix chain 'A' and resid 2825 through 2836 Processing helix chain 'A' and resid 2841 through 2844 Processing helix chain 'A' and resid 2846 through 2863 removed outlier: 3.625A pdb=" N LYS A2851 " --> pdb=" O GLU A2848 " (cutoff:3.500A) Processing helix chain 'A' and resid 2870 through 2884 Processing helix chain 'A' and resid 2897 through 2904 Processing helix chain 'A' and resid 2906 through 2909 No H-bonds generated for 'chain 'A' and resid 2906 through 2909' Processing helix chain 'A' and resid 2922 through 2935 removed outlier: 4.176A pdb=" N VAL A2935 " --> pdb=" O ASN A2931 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2944 No H-bonds generated for 'chain 'A' and resid 2942 through 2944' Processing helix chain 'A' and resid 2961 through 2979 Processing helix chain 'A' and resid 2990 through 3021 removed outlier: 3.655A pdb=" N VAL A3000 " --> pdb=" O LEU A2996 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A3001 " --> pdb=" O ARG A2997 " (cutoff:3.500A) Processing helix chain 'A' and resid 3306 through 3336 removed outlier: 3.674A pdb=" N ILE A3321 " --> pdb=" O SER A3317 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A3322 " --> pdb=" O GLN A3318 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A3325 " --> pdb=" O ILE A3321 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A3326 " --> pdb=" O GLY A3322 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY A3335 " --> pdb=" O GLU A3331 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS A3336 " --> pdb=" O THR A3332 " (cutoff:3.500A) Processing helix chain 'A' and resid 3339 through 3355 removed outlier: 3.677A pdb=" N LEU A3352 " --> pdb=" O ILE A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3366 through 3370 Processing helix chain 'A' and resid 3373 through 3381 removed outlier: 3.968A pdb=" N LEU A3380 " --> pdb=" O LYS A3376 " (cutoff:3.500A) Processing helix chain 'A' and resid 3388 through 3399 Processing helix chain 'A' and resid 3414 through 3425 removed outlier: 4.181A pdb=" N SER A3419 " --> pdb=" O ILE A3415 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN A3424 " --> pdb=" O ASN A3420 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LYS A3425 " --> pdb=" O TYR A3421 " (cutoff:3.500A) Processing helix chain 'A' and resid 3436 through 3446 Processing helix chain 'A' and resid 3460 through 3466 removed outlier: 4.281A pdb=" N ARG A3464 " --> pdb=" O ILE A3461 " (cutoff:3.500A) Processing helix chain 'A' and resid 3507 through 3510 No H-bonds generated for 'chain 'A' and resid 3507 through 3510' Processing helix chain 'A' and resid 3522 through 3537 removed outlier: 4.583A pdb=" N ILE A3529 " --> pdb=" O GLU A3526 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE A3530 " --> pdb=" O THR A3527 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A3534 " --> pdb=" O ASP A3531 " (cutoff:3.500A) Processing helix chain 'A' and resid 3539 through 3567 removed outlier: 3.650A pdb=" N GLU A3546 " --> pdb=" O GLN A3542 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE A3549 " --> pdb=" O ARG A3545 " (cutoff:3.500A) Processing helix chain 'A' and resid 3587 through 3613 removed outlier: 3.840A pdb=" N LEU A3601 " --> pdb=" O ILE A3597 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER A3604 " --> pdb=" O LYS A3600 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A3607 " --> pdb=" O GLU A3603 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A3608 " --> pdb=" O SER A3604 " (cutoff:3.500A) Proline residue: A3609 - end of helix Processing helix chain 'A' and resid 3616 through 3638 removed outlier: 3.636A pdb=" N HIS A3624 " --> pdb=" O ILE A3620 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A3627 " --> pdb=" O LYS A3623 " (cutoff:3.500A) Processing helix chain 'A' and resid 3646 through 3656 removed outlier: 3.721A pdb=" N ARG A3655 " --> pdb=" O SER A3651 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A3656 " --> pdb=" O CYS A3652 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3686 removed outlier: 3.884A pdb=" N TRP A3676 " --> pdb=" O ASP A3672 " (cutoff:3.500A) Processing helix chain 'A' and resid 3692 through 3710 removed outlier: 4.491A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A3710 " --> pdb=" O TYR A3706 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3726 Processing helix chain 'A' and resid 3746 through 3752 Processing helix chain 'A' and resid 3757 through 3767 removed outlier: 4.213A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A3767 " --> pdb=" O PHE A3763 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3780 Processing helix chain 'A' and resid 3797 through 3807 removed outlier: 3.528A pdb=" N GLU A3802 " --> pdb=" O PHE A3798 " (cutoff:3.500A) Processing helix chain 'A' and resid 3819 through 3835 removed outlier: 4.349A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3848 through 3853 removed outlier: 3.641A pdb=" N THR A3853 " --> pdb=" O SER A3849 " (cutoff:3.500A) Processing helix chain 'A' and resid 3855 through 3860 Processing helix chain 'A' and resid 3886 through 3891 Processing helix chain 'A' and resid 3903 through 3917 removed outlier: 3.535A pdb=" N SER A3913 " --> pdb=" O ASP A3909 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A3914 " --> pdb=" O LEU A3910 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A3915 " --> pdb=" O TRP A3911 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE A3916 " --> pdb=" O GLY A3912 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR A3917 " --> pdb=" O SER A3913 " (cutoff:3.500A) Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 3.535A pdb=" N TYR A3927 " --> pdb=" O VAL A3923 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3958 through 3973 Processing helix chain 'A' and resid 3980 through 3991 removed outlier: 4.311A pdb=" N VAL A3985 " --> pdb=" O TRP A3982 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A3986 " --> pdb=" O ALA A3983 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A3987 " --> pdb=" O GLN A3984 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A3991 " --> pdb=" O HIS A3988 " (cutoff:3.500A) Processing helix chain 'A' and resid 4001 through 4014 removed outlier: 3.564A pdb=" N HIS A4013 " --> pdb=" O LYS A4009 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4050 Processing helix chain 'A' and resid 4058 through 4061 No H-bonds generated for 'chain 'A' and resid 4058 through 4061' Processing helix chain 'A' and resid 4067 through 4091 Processing sheet with id= A, first strand: chain 'A' and resid 1385 through 1387 Processing sheet with id= B, first strand: chain 'A' and resid 1589 through 1591 removed outlier: 3.832A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id= D, first strand: chain 'A' and resid 1916 through 1920 removed outlier: 7.401A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id= F, first strand: chain 'A' and resid 2211 through 2215 removed outlier: 8.360A pdb=" N LEU A2070 " --> pdb=" O PHE A2190 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A2192 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU A2072 " --> pdb=" O ILE A2192 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE A2194 " --> pdb=" O LEU A2072 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY A2074 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A2196 " --> pdb=" O GLY A2074 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id= H, first strand: chain 'A' and resid 2358 through 2362 removed outlier: 3.965A pdb=" N SER A2367 " --> pdb=" O ALA A2362 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2554 through 2559 removed outlier: 7.043A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU A2559 " --> pdb=" O ILE A2415 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N CYS A2417 " --> pdb=" O LEU A2559 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A2414 " --> pdb=" O ILE A2531 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2465 through 2467 Processing sheet with id= K, first strand: chain 'A' and resid 2912 through 2917 removed outlier: 6.821A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 3514 through 3517 removed outlier: 7.887A pdb=" N LEU A3494 " --> pdb=" O PRO A3405 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N LEU A3407 " --> pdb=" O LEU A3494 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE A3496 " --> pdb=" O LEU A3407 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 3478 through 3481 removed outlier: 3.650A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 3893 through 3896 removed outlier: 6.544A pdb=" N MET A3873 " --> pdb=" O PHE A3786 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N MET A3788 " --> pdb=" O MET A3873 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET A3875 " --> pdb=" O MET A3788 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER A3790 " --> pdb=" O MET A3875 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS A3877 " --> pdb=" O SER A3790 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN A3842 " --> pdb=" O LYS A3812 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A3814 " --> pdb=" O GLN A3842 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2646 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: 10.62 Time building geometry restraints manager: 8.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.29: 3270 1.29 - 1.45: 5710 1.45 - 1.61: 10933 1.61 - 1.78: 27 1.78 - 1.94: 122 Bond restraints: 20062 Sorted by residual: bond pdb=" C14 ZG7 A4201 " pdb=" N15 ZG7 A4201 " ideal model delta sigma weight residual 1.328 1.527 -0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" C14 ZG7 A4202 " pdb=" N15 ZG7 A4202 " ideal model delta sigma weight residual 1.328 1.509 -0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" C26 ZG7 A4201 " pdb=" O27 ZG7 A4201 " ideal model delta sigma weight residual 1.305 1.154 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C4 ATP A4203 " pdb=" C5 ATP A4203 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.02e+01 bond pdb=" C16 ZG7 A4201 " pdb=" N15 ZG7 A4201 " ideal model delta sigma weight residual 1.312 1.444 -0.132 2.00e-02 2.50e+03 4.39e+01 ... (remaining 20057 not shown) Histogram of bond angle deviations from ideal: 59.60 - 83.56: 6 83.56 - 107.51: 900 107.51 - 131.46: 26163 131.46 - 155.41: 65 155.41 - 179.37: 2 Bond angle restraints: 27136 Sorted by residual: angle pdb=" PA ATP A4203 " pdb=" O3A ATP A4203 " pdb=" PB ATP A4203 " ideal model delta sigma weight residual 136.83 121.05 15.78 1.00e+00 1.00e+00 2.49e+02 angle pdb=" PB ATP A4203 " pdb=" O3B ATP A4203 " pdb=" PG ATP A4203 " ideal model delta sigma weight residual 139.87 128.76 11.11 1.00e+00 1.00e+00 1.23e+02 angle pdb=" C5 ATP A4203 " pdb=" C4 ATP A4203 " pdb=" N3 ATP A4203 " ideal model delta sigma weight residual 126.80 118.15 8.65 1.00e+00 1.00e+00 7.49e+01 angle pdb=" N3 ATP A4203 " pdb=" C4 ATP A4203 " pdb=" N9 ATP A4203 " ideal model delta sigma weight residual 127.04 136.74 -9.70 1.15e+00 7.59e-01 7.13e+01 angle pdb=" O1G ATP A4203 " pdb=" PG ATP A4203 " pdb=" O3B ATP A4203 " ideal model delta sigma weight residual 110.47 98.96 11.51 1.64e+00 3.70e-01 4.90e+01 ... (remaining 27131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11158 17.98 - 35.96: 683 35.96 - 53.94: 148 53.94 - 71.91: 49 71.91 - 89.89: 28 Dihedral angle restraints: 12066 sinusoidal: 4964 harmonic: 7102 Sorted by residual: dihedral pdb=" CA ASP A2105 " pdb=" C ASP A2105 " pdb=" N THR A2106 " pdb=" CA THR A2106 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLN A2639 " pdb=" C GLN A2639 " pdb=" N THR A2640 " pdb=" CA THR A2640 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" N VAL A3615 " pdb=" C VAL A3615 " pdb=" CA VAL A3615 " pdb=" CB VAL A3615 " ideal model delta harmonic sigma weight residual 123.40 135.08 -11.68 0 2.50e+00 1.60e-01 2.18e+01 ... (remaining 12063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2172 0.076 - 0.153: 736 0.153 - 0.229: 129 0.229 - 0.305: 18 0.305 - 0.382: 10 Chirality restraints: 3065 Sorted by residual: chirality pdb=" CB ILE A2141 " pdb=" CA ILE A2141 " pdb=" CG1 ILE A2141 " pdb=" CG2 ILE A2141 " both_signs ideal model delta sigma weight residual False 2.64 3.03 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA PHE A2943 " pdb=" N PHE A2943 " pdb=" C PHE A2943 " pdb=" CB PHE A2943 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CB VAL A2984 " pdb=" CA VAL A2984 " pdb=" CG1 VAL A2984 " pdb=" CG2 VAL A2984 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3062 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 ZG7 A4201 " -0.017 2.00e-02 2.50e+03 4.17e-02 6.08e+01 pdb=" C11 ZG7 A4201 " 0.092 2.00e-02 2.50e+03 pdb=" C14 ZG7 A4201 " -0.011 2.00e-02 2.50e+03 pdb=" C16 ZG7 A4201 " -0.021 2.00e-02 2.50e+03 pdb=" C17 ZG7 A4201 " -0.030 2.00e-02 2.50e+03 pdb=" C26 ZG7 A4201 " 0.006 2.00e-02 2.50e+03 pdb=" C28 ZG7 A4201 " -0.031 2.00e-02 2.50e+03 pdb=" C29 ZG7 A4201 " 0.006 2.00e-02 2.50e+03 pdb=" N12 ZG7 A4201 " -0.007 2.00e-02 2.50e+03 pdb=" N13 ZG7 A4201 " -0.049 2.00e-02 2.50e+03 pdb=" N15 ZG7 A4201 " -0.013 2.00e-02 2.50e+03 pdb=" N30 ZG7 A4201 " 0.021 2.00e-02 2.50e+03 pdb=" O18 ZG7 A4201 " 0.093 2.00e-02 2.50e+03 pdb=" O27 ZG7 A4201 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2916 " -0.027 2.00e-02 2.50e+03 3.57e-02 3.19e+01 pdb=" CG TRP A2916 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP A2916 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A2916 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A2916 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP A2916 " 0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP A2916 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2916 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2916 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP A2916 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A2857 " -0.028 2.00e-02 2.50e+03 5.61e-02 3.14e+01 pdb=" C ARG A2857 " 0.097 2.00e-02 2.50e+03 pdb=" O ARG A2857 " -0.037 2.00e-02 2.50e+03 pdb=" N ASN A2858 " -0.033 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 220 2.60 - 3.18: 17746 3.18 - 3.75: 31025 3.75 - 4.33: 41723 4.33 - 4.90: 67770 Nonbonded interactions: 158484 Sorted by model distance: nonbonded pdb=" O3G ATP A4203 " pdb="MG MG A4204 " model vdw 2.027 2.170 nonbonded pdb=" O1B ATP A4203 " pdb="MG MG A4204 " model vdw 2.042 2.170 nonbonded pdb=" OG1 THR A2081 " pdb="MG MG A4204 " model vdw 2.079 2.170 nonbonded pdb=" O ARG A3445 " pdb=" OG SER A3489 " model vdw 2.122 2.440 nonbonded pdb=" O ASP A3531 " pdb=" OG1 THR A3535 " model vdw 2.195 2.440 ... (remaining 158479 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=0.50 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 11.730 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 56.290 Find NCS groups from input model: 0.750 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 0.199 20062 Z= 0.789 Angle : 1.493 22.111 27136 Z= 0.823 Chirality : 0.078 0.382 3065 Planarity : 0.009 0.056 3416 Dihedral : 13.680 89.891 7458 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.27 % Favored : 94.32 % Rotamer: Outliers : 1.32 % Allowed : 4.99 % Favored : 93.69 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: -2.30 (0.14), residues: 2411 helix: -1.13 (0.12), residues: 1373 sheet: -1.33 (0.35), residues: 194 loop : -1.99 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.006 TRP A2916 HIS 0.043 0.004 HIS A1554 PHE 0.084 0.005 PHE A3446 TYR 0.039 0.005 TYR A2356 ARG 0.035 0.002 ARG A2830 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 568 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1409 LEU cc_start: 0.9479 (mt) cc_final: 0.9265 (mp) REVERT: A 1466 GLN cc_start: 0.8711 (pt0) cc_final: 0.8480 (pt0) REVERT: A 1509 LEU cc_start: 0.8845 (mt) cc_final: 0.8418 (mt) REVERT: A 1510 LYS cc_start: 0.8938 (mttp) cc_final: 0.8736 (tppt) REVERT: A 1650 LEU cc_start: 0.9242 (tp) cc_final: 0.9006 (tt) REVERT: A 1848 ASP cc_start: 0.8370 (t0) cc_final: 0.8089 (p0) REVERT: A 1919 PHE cc_start: 0.8172 (t80) cc_final: 0.6387 (t80) REVERT: A 2091 MET cc_start: 0.8010 (mtt) cc_final: 0.7363 (mpp) REVERT: A 2157 ASP cc_start: 0.7508 (p0) cc_final: 0.7301 (p0) REVERT: A 2169 VAL cc_start: 0.8901 (t) cc_final: 0.8644 (m) REVERT: A 2171 ASP cc_start: 0.8850 (m-30) cc_final: 0.8604 (m-30) REVERT: A 2190 PHE cc_start: 0.7149 (t80) cc_final: 0.6821 (t80) REVERT: A 2213 LEU cc_start: 0.8411 (tp) cc_final: 0.7981 (mp) REVERT: A 2225 LYS cc_start: 0.8684 (tttt) cc_final: 0.8377 (tttt) REVERT: A 2317 LEU cc_start: 0.9591 (mt) cc_final: 0.9390 (tt) REVERT: A 2549 ARG cc_start: 0.6650 (mtp180) cc_final: 0.5643 (mtp180) REVERT: A 2805 ASP cc_start: 0.8182 (m-30) cc_final: 0.7977 (m-30) REVERT: A 2914 ILE cc_start: 0.9286 (mt) cc_final: 0.8917 (mt) REVERT: A 2960 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8325 (p) REVERT: A 3012 GLU cc_start: 0.9455 (tm-30) cc_final: 0.8931 (tm-30) REVERT: A 3013 ASN cc_start: 0.9556 (t0) cc_final: 0.9242 (t0) REVERT: A 3014 GLN cc_start: 0.9441 (pt0) cc_final: 0.9112 (pt0) REVERT: A 3015 ARG cc_start: 0.9149 (ttp-170) cc_final: 0.8629 (ttp80) REVERT: A 3016 PHE cc_start: 0.9452 (t80) cc_final: 0.9108 (t80) REVERT: A 3308 ASN cc_start: 0.8599 (t0) cc_final: 0.8085 (t0) REVERT: A 3316 THR cc_start: 0.9786 (m) cc_final: 0.9581 (m) REVERT: A 3538 ASN cc_start: 0.8969 (t0) cc_final: 0.8747 (t0) REVERT: A 3541 MET cc_start: 0.8666 (mmm) cc_final: 0.8039 (mmm) REVERT: A 3621 ILE cc_start: 0.9255 (mt) cc_final: 0.8968 (mt) REVERT: A 3655 ARG cc_start: 0.8871 (mtp-110) cc_final: 0.8625 (mtp85) REVERT: A 3681 GLU cc_start: 0.9247 (tp30) cc_final: 0.8617 (tp30) REVERT: A 3700 MET cc_start: 0.8509 (ttm) cc_final: 0.8232 (ttp) REVERT: A 3717 GLU cc_start: 0.9003 (tp30) cc_final: 0.8717 (pp20) REVERT: A 3745 ARG cc_start: 0.7647 (tpt170) cc_final: 0.7295 (mmp-170) REVERT: A 3749 ASP cc_start: 0.8469 (m-30) cc_final: 0.8041 (t0) REVERT: A 3767 PHE cc_start: 0.7846 (m-80) cc_final: 0.7474 (m-80) REVERT: A 3803 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9060 (pp) REVERT: A 3873 MET cc_start: 0.8595 (ttp) cc_final: 0.8304 (ttm) REVERT: A 3952 LYS cc_start: 0.8851 (ptmm) cc_final: 0.8573 (tmtt) outliers start: 29 outliers final: 10 residues processed: 589 average time/residue: 0.3525 time to fit residues: 304.8675 Evaluate side-chains 308 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 296 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1495 THR Chi-restraints excluded: chain A residue 1793 CYS Chi-restraints excluded: chain A residue 2059 GLN Chi-restraints excluded: chain A residue 2131 THR Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2702 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2960 THR Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3803 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1372 ASN ** A1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1449 GLN A1667 ASN A1757 GLN A1869 GLN A2201 HIS A2300 GLN A2363 ASN A2500 GLN ** A2508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2569 GLN A2832 ASN A2854 ASN A3013 ASN A3308 ASN ** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3596 ASN A3784 ASN A3948 HIS ** A3988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4077 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20062 Z= 0.289 Angle : 0.726 11.396 27136 Z= 0.378 Chirality : 0.044 0.281 3065 Planarity : 0.004 0.046 3416 Dihedral : 7.269 83.948 2660 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 3.18 % Allowed : 13.79 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.16), residues: 2411 helix: 0.56 (0.14), residues: 1375 sheet: -1.01 (0.35), residues: 194 loop : -1.52 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A2084 HIS 0.011 0.001 HIS A3517 PHE 0.031 0.002 PHE A1491 TYR 0.029 0.002 TYR A2674 ARG 0.007 0.001 ARG A2594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 327 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1466 GLN cc_start: 0.8725 (pt0) cc_final: 0.8299 (mt0) REVERT: A 1510 LYS cc_start: 0.8932 (mttp) cc_final: 0.8727 (tppt) REVERT: A 1655 MET cc_start: 0.8721 (ttm) cc_final: 0.8206 (tmm) REVERT: A 1813 LEU cc_start: 0.9499 (tt) cc_final: 0.9121 (mt) REVERT: A 1937 MET cc_start: 0.4486 (mmm) cc_final: 0.3552 (mtt) REVERT: A 2105 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6154 (m-30) REVERT: A 2118 MET cc_start: 0.8336 (pmm) cc_final: 0.7801 (tpt) REVERT: A 2127 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: A 2155 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7180 (p0) REVERT: A 2171 ASP cc_start: 0.8724 (m-30) cc_final: 0.8504 (m-30) REVERT: A 2213 LEU cc_start: 0.8309 (tp) cc_final: 0.7981 (mp) REVERT: A 2549 ARG cc_start: 0.6723 (mtp180) cc_final: 0.5611 (mtp180) REVERT: A 2792 LEU cc_start: 0.9183 (mt) cc_final: 0.8618 (mp) REVERT: A 2871 GLN cc_start: 0.9020 (mp10) cc_final: 0.8757 (mp10) REVERT: A 3013 ASN cc_start: 0.9584 (t0) cc_final: 0.9262 (t0) REVERT: A 3014 GLN cc_start: 0.9441 (pt0) cc_final: 0.9109 (pt0) REVERT: A 3330 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8671 (t80) REVERT: A 3538 ASN cc_start: 0.8977 (t0) cc_final: 0.8695 (t0) REVERT: A 3541 MET cc_start: 0.8570 (mmm) cc_final: 0.8053 (mmm) REVERT: A 3600 LYS cc_start: 0.8783 (pttm) cc_final: 0.8572 (pttm) REVERT: A 3633 GLU cc_start: 0.9061 (tp30) cc_final: 0.8779 (tp30) REVERT: A 3681 GLU cc_start: 0.9154 (tp30) cc_final: 0.8899 (tp30) REVERT: A 3717 GLU cc_start: 0.9068 (tp30) cc_final: 0.8721 (pp20) REVERT: A 3722 MET cc_start: 0.8789 (mmm) cc_final: 0.8378 (mmm) REVERT: A 3736 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.5234 (pp) REVERT: A 3745 ARG cc_start: 0.7941 (tpt170) cc_final: 0.7446 (tpp-160) REVERT: A 3816 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8731 (tp) REVERT: A 3910 LEU cc_start: 0.9504 (mp) cc_final: 0.9257 (mp) outliers start: 70 outliers final: 34 residues processed: 370 average time/residue: 0.3351 time to fit residues: 188.1656 Evaluate side-chains 288 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 248 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1449 GLN Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2127 ASP Chi-restraints excluded: chain A residue 2155 ASP Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2166 MET Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2603 CYS Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2700 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2860 THR Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3472 HIS Chi-restraints excluded: chain A residue 3479 VAL Chi-restraints excluded: chain A residue 3487 ASP Chi-restraints excluded: chain A residue 3491 ASP Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3693 LYS Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3816 LEU Chi-restraints excluded: chain A residue 3907 VAL Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 196 optimal weight: 0.9990 chunk 218 optimal weight: 0.0040 chunk 75 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1372 ASN A1444 ASN A2508 GLN ** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3561 ASN A3596 ASN A4090 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20062 Z= 0.159 Angle : 0.650 13.448 27136 Z= 0.325 Chirality : 0.042 0.272 3065 Planarity : 0.004 0.046 3416 Dihedral : 6.495 88.857 2647 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.72 % Rotamer: Outliers : 2.27 % Allowed : 14.93 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.17), residues: 2411 helix: 0.99 (0.14), residues: 1368 sheet: -0.67 (0.36), residues: 194 loop : -1.27 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A2125 HIS 0.008 0.001 HIS A2228 PHE 0.023 0.001 PHE A3767 TYR 0.021 0.001 TYR A3369 ARG 0.007 0.001 ARG A2646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 328 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1497 ILE cc_start: 0.9357 (tp) cc_final: 0.9075 (mt) REVERT: A 1510 LYS cc_start: 0.8943 (mttp) cc_final: 0.8729 (tppt) REVERT: A 1608 LEU cc_start: 0.9408 (mt) cc_final: 0.9144 (mt) REVERT: A 1704 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8991 (mt-10) REVERT: A 1823 ASP cc_start: 0.7560 (t0) cc_final: 0.7356 (t0) REVERT: A 1919 PHE cc_start: 0.7641 (t80) cc_final: 0.7338 (t80) REVERT: A 1937 MET cc_start: 0.4623 (mmm) cc_final: 0.3746 (mtt) REVERT: A 1992 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7044 (tptt) REVERT: A 2063 MET cc_start: 0.9061 (tpp) cc_final: 0.8702 (tpp) REVERT: A 2118 MET cc_start: 0.8335 (pmm) cc_final: 0.7735 (tpt) REVERT: A 2171 ASP cc_start: 0.8817 (m-30) cc_final: 0.8608 (m-30) REVERT: A 2213 LEU cc_start: 0.8306 (tp) cc_final: 0.8009 (mp) REVERT: A 2549 ARG cc_start: 0.6568 (mtp180) cc_final: 0.5443 (mtp180) REVERT: A 2618 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.9106 (t) REVERT: A 2792 LEU cc_start: 0.9087 (mt) cc_final: 0.8287 (mp) REVERT: A 2871 GLN cc_start: 0.8966 (mp10) cc_final: 0.8655 (mp10) REVERT: A 3013 ASN cc_start: 0.9514 (t0) cc_final: 0.9180 (t0) REVERT: A 3015 ARG cc_start: 0.9088 (ttp-170) cc_final: 0.8544 (ttp80) REVERT: A 3311 LYS cc_start: 0.9282 (tmmt) cc_final: 0.8996 (tmmt) REVERT: A 3379 TRP cc_start: 0.9170 (m-10) cc_final: 0.8831 (m-10) REVERT: A 3414 MET cc_start: 0.8719 (mmm) cc_final: 0.8405 (mmp) REVERT: A 3538 ASN cc_start: 0.8964 (t0) cc_final: 0.8723 (t0) REVERT: A 3541 MET cc_start: 0.8605 (mmm) cc_final: 0.8110 (mmm) REVERT: A 3677 LEU cc_start: 0.8923 (mm) cc_final: 0.8472 (tt) REVERT: A 3681 GLU cc_start: 0.9050 (tp30) cc_final: 0.8705 (tp30) REVERT: A 3717 GLU cc_start: 0.9049 (tp30) cc_final: 0.8702 (pp20) REVERT: A 3736 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5518 (pp) REVERT: A 3875 MET cc_start: 0.7658 (mpp) cc_final: 0.7118 (mpp) outliers start: 50 outliers final: 21 residues processed: 360 average time/residue: 0.3138 time to fit residues: 174.3344 Evaluate side-chains 290 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 266 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1560 LYS Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2164 GLU Chi-restraints excluded: chain A residue 2173 ASN Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2860 THR Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3472 HIS Chi-restraints excluded: chain A residue 3487 ASP Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3693 LYS Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 209 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 GLN A2173 ASN ** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4090 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20062 Z= 0.282 Angle : 0.674 12.878 27136 Z= 0.343 Chirality : 0.043 0.277 3065 Planarity : 0.004 0.047 3416 Dihedral : 6.481 82.091 2645 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 3.45 % Allowed : 15.88 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.17), residues: 2411 helix: 1.05 (0.14), residues: 1368 sheet: -0.75 (0.37), residues: 187 loop : -1.19 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A2084 HIS 0.012 0.001 HIS A3517 PHE 0.021 0.002 PHE A2190 TYR 0.017 0.002 TYR A3679 ARG 0.005 0.001 ARG A2586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 255 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1447 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8734 (mp0) REVERT: A 1704 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8995 (mt-10) REVERT: A 1813 LEU cc_start: 0.9497 (tt) cc_final: 0.9049 (mp) REVERT: A 1919 PHE cc_start: 0.8143 (t80) cc_final: 0.7915 (t80) REVERT: A 1992 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7025 (tptt) REVERT: A 2063 MET cc_start: 0.9110 (tpp) cc_final: 0.8780 (tpp) REVERT: A 2118 MET cc_start: 0.8456 (pmm) cc_final: 0.7878 (tpt) REVERT: A 2213 LEU cc_start: 0.8425 (tp) cc_final: 0.8057 (mp) REVERT: A 2756 MET cc_start: 0.8875 (tpp) cc_final: 0.8364 (ttt) REVERT: A 2871 GLN cc_start: 0.8967 (mp10) cc_final: 0.8640 (mp10) REVERT: A 3013 ASN cc_start: 0.9523 (t0) cc_final: 0.9068 (t0) REVERT: A 3015 ARG cc_start: 0.9078 (ttp-170) cc_final: 0.8703 (ttp80) REVERT: A 3313 PHE cc_start: 0.8843 (t80) cc_final: 0.8306 (t80) REVERT: A 3330 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8753 (t80) REVERT: A 3414 MET cc_start: 0.8886 (mmm) cc_final: 0.8624 (mmm) REVERT: A 3541 MET cc_start: 0.8606 (mmm) cc_final: 0.8182 (mmm) REVERT: A 3677 LEU cc_start: 0.8915 (mm) cc_final: 0.8431 (tt) REVERT: A 3717 GLU cc_start: 0.9108 (tp30) cc_final: 0.8699 (pp20) REVERT: A 3736 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5622 (pp) REVERT: A 3910 LEU cc_start: 0.9499 (mp) cc_final: 0.9274 (mp) outliers start: 76 outliers final: 45 residues processed: 307 average time/residue: 0.3109 time to fit residues: 149.0085 Evaluate side-chains 280 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 232 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1560 LYS Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1955 LEU Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2173 ASN Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2603 CYS Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2631 THR Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2860 THR Chi-restraints excluded: chain A residue 2917 MET Chi-restraints excluded: chain A residue 2921 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3483 ASP Chi-restraints excluded: chain A residue 3487 ASP Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3513 VAL Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3693 LYS Chi-restraints excluded: chain A residue 3736 LEU Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3907 VAL Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 4089 LEU Chi-restraints excluded: chain A residue 4090 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 209 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1554 HIS A2461 HIS A3399 ASN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3596 ASN ** A3648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20062 Z= 0.215 Angle : 0.643 14.435 27136 Z= 0.322 Chirality : 0.041 0.222 3065 Planarity : 0.004 0.052 3416 Dihedral : 6.283 83.224 2645 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 2.99 % Allowed : 17.20 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.17), residues: 2411 helix: 1.14 (0.14), residues: 1366 sheet: -0.73 (0.36), residues: 192 loop : -1.09 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A2084 HIS 0.008 0.001 HIS A3517 PHE 0.020 0.001 PHE A3768 TYR 0.026 0.001 TYR A3369 ARG 0.004 0.000 ARG A2646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 261 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1506 ASP cc_start: 0.8165 (p0) cc_final: 0.7948 (p0) REVERT: A 1704 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8951 (mt-10) REVERT: A 1813 LEU cc_start: 0.9479 (tt) cc_final: 0.9040 (mp) REVERT: A 1937 MET cc_start: 0.4555 (mmm) cc_final: 0.3600 (mtt) REVERT: A 1992 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6998 (tptt) REVERT: A 2063 MET cc_start: 0.9085 (tpp) cc_final: 0.8818 (tpp) REVERT: A 2118 MET cc_start: 0.8546 (pmm) cc_final: 0.7902 (tpt) REVERT: A 2157 ASP cc_start: 0.7435 (p0) cc_final: 0.7221 (p0) REVERT: A 2213 LEU cc_start: 0.8470 (tp) cc_final: 0.8117 (mp) REVERT: A 2756 MET cc_start: 0.8867 (tpp) cc_final: 0.8344 (ttt) REVERT: A 2792 LEU cc_start: 0.9245 (mt) cc_final: 0.8836 (mp) REVERT: A 2871 GLN cc_start: 0.8958 (mp10) cc_final: 0.8640 (mp10) REVERT: A 3013 ASN cc_start: 0.9504 (t0) cc_final: 0.9069 (t0) REVERT: A 3015 ARG cc_start: 0.9072 (ttp-170) cc_final: 0.8690 (ttp80) REVERT: A 3313 PHE cc_start: 0.8879 (t80) cc_final: 0.8341 (t80) REVERT: A 3330 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8739 (t80) REVERT: A 3541 MET cc_start: 0.8696 (mmm) cc_final: 0.8312 (mmm) REVERT: A 3677 LEU cc_start: 0.8904 (mm) cc_final: 0.8438 (tt) REVERT: A 3679 TYR cc_start: 0.9321 (m-80) cc_final: 0.8909 (m-80) REVERT: A 3717 GLU cc_start: 0.9122 (tp30) cc_final: 0.8676 (pp20) REVERT: A 3722 MET cc_start: 0.8726 (mmm) cc_final: 0.8432 (mmm) REVERT: A 3910 LEU cc_start: 0.9476 (mp) cc_final: 0.9222 (mp) outliers start: 66 outliers final: 39 residues processed: 305 average time/residue: 0.2975 time to fit residues: 142.9338 Evaluate side-chains 284 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1560 LYS Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2155 ASP Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2860 THR Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3487 ASP Chi-restraints excluded: chain A residue 3491 ASP Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3873 MET Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4089 LEU Chi-restraints excluded: chain A residue 4090 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 10.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1557 GLN A2173 ASN A2270 ASN A3596 ASN ** A3648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4090 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20062 Z= 0.210 Angle : 0.637 13.221 27136 Z= 0.318 Chirality : 0.041 0.296 3065 Planarity : 0.004 0.055 3416 Dihedral : 6.133 83.441 2644 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.50 % Allowed : 18.24 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.17), residues: 2411 helix: 1.25 (0.14), residues: 1357 sheet: -0.68 (0.37), residues: 192 loop : -1.05 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A2084 HIS 0.007 0.001 HIS A3517 PHE 0.020 0.001 PHE A3768 TYR 0.022 0.001 TYR A3369 ARG 0.004 0.000 ARG A2788 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8948 (mt-10) REVERT: A 1992 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7004 (tptt) REVERT: A 2063 MET cc_start: 0.9089 (tpp) cc_final: 0.8853 (tpp) REVERT: A 2157 ASP cc_start: 0.7435 (p0) cc_final: 0.7212 (p0) REVERT: A 2213 LEU cc_start: 0.8556 (tp) cc_final: 0.8143 (mp) REVERT: A 2496 LYS cc_start: 0.9222 (tptp) cc_final: 0.8579 (pttm) REVERT: A 2756 MET cc_start: 0.8861 (tpp) cc_final: 0.8337 (ttt) REVERT: A 2871 GLN cc_start: 0.8957 (mp10) cc_final: 0.8628 (mp10) REVERT: A 3013 ASN cc_start: 0.9489 (t0) cc_final: 0.9171 (t0) REVERT: A 3015 ARG cc_start: 0.9069 (ttp-170) cc_final: 0.8672 (ttp80) REVERT: A 3313 PHE cc_start: 0.8922 (t80) cc_final: 0.8625 (t80) REVERT: A 3330 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8735 (t80) REVERT: A 3414 MET cc_start: 0.8708 (mmp) cc_final: 0.8473 (mmp) REVERT: A 3541 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8297 (mmm) REVERT: A 3717 GLU cc_start: 0.9124 (tp30) cc_final: 0.8655 (pp20) outliers start: 55 outliers final: 44 residues processed: 300 average time/residue: 0.3382 time to fit residues: 162.3765 Evaluate side-chains 288 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1560 LYS Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2155 ASP Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 ASN Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2603 CYS Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2711 ASP Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2860 THR Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2959 GLN Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3487 ASP Chi-restraints excluded: chain A residue 3491 ASP Chi-restraints excluded: chain A residue 3541 MET Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 133 optimal weight: 0.0470 chunk 170 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 197 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20062 Z= 0.166 Angle : 0.637 14.471 27136 Z= 0.314 Chirality : 0.041 0.230 3065 Planarity : 0.003 0.055 3416 Dihedral : 5.975 83.965 2644 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.32 % Favored : 96.60 % Rotamer: Outliers : 2.59 % Allowed : 18.69 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.17), residues: 2411 helix: 1.36 (0.14), residues: 1356 sheet: -0.64 (0.37), residues: 192 loop : -1.02 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2084 HIS 0.006 0.001 HIS A3517 PHE 0.025 0.001 PHE A3611 TYR 0.021 0.001 TYR A3369 ARG 0.004 0.000 ARG A2788 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 267 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1415 MET cc_start: 0.8677 (mtt) cc_final: 0.8348 (ptp) REVERT: A 1447 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8759 (mp0) REVERT: A 1704 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8894 (mt-10) REVERT: A 1919 PHE cc_start: 0.8061 (t80) cc_final: 0.7579 (t80) REVERT: A 1936 ILE cc_start: 0.8927 (mt) cc_final: 0.8537 (mt) REVERT: A 1937 MET cc_start: 0.4537 (mmm) cc_final: 0.3616 (mtt) REVERT: A 1992 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7005 (tptt) REVERT: A 2157 ASP cc_start: 0.7401 (p0) cc_final: 0.7176 (p0) REVERT: A 2213 LEU cc_start: 0.8541 (tp) cc_final: 0.8163 (mp) REVERT: A 2496 LYS cc_start: 0.9209 (tptp) cc_final: 0.8585 (pttm) REVERT: A 2756 MET cc_start: 0.8863 (tpp) cc_final: 0.8284 (ttt) REVERT: A 2792 LEU cc_start: 0.9211 (mt) cc_final: 0.8791 (mp) REVERT: A 2871 GLN cc_start: 0.8959 (mp10) cc_final: 0.8662 (mp10) REVERT: A 3013 ASN cc_start: 0.9468 (t0) cc_final: 0.9162 (t0) REVERT: A 3015 ARG cc_start: 0.9069 (ttp-170) cc_final: 0.8504 (ttp80) REVERT: A 3311 LYS cc_start: 0.9156 (tmmt) cc_final: 0.8812 (tmmt) REVERT: A 3313 PHE cc_start: 0.8931 (t80) cc_final: 0.8617 (t80) REVERT: A 3330 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8748 (t80) REVERT: A 3414 MET cc_start: 0.8666 (mmp) cc_final: 0.8352 (mmm) REVERT: A 3541 MET cc_start: 0.8711 (mmm) cc_final: 0.8348 (mmm) REVERT: A 3655 ARG cc_start: 0.8904 (ttm110) cc_final: 0.8659 (ttp-110) REVERT: A 3702 MET cc_start: 0.8785 (mmm) cc_final: 0.8332 (mmm) REVERT: A 3717 GLU cc_start: 0.9149 (tp30) cc_final: 0.8648 (pp20) REVERT: A 3910 LEU cc_start: 0.9432 (mp) cc_final: 0.9217 (mp) outliers start: 57 outliers final: 44 residues processed: 307 average time/residue: 0.3009 time to fit residues: 145.8225 Evaluate side-chains 292 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 246 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1560 LYS Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 ASN Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2603 CYS Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2860 THR Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2959 GLN Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3487 ASP Chi-restraints excluded: chain A residue 3491 ASP Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 158 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 21 optimal weight: 0.0270 chunk 183 optimal weight: 0.3980 chunk 212 optimal weight: 9.9990 overall best weight: 5.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1466 GLN ** A1870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2173 ASN A2461 HIS ** A3648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20062 Z= 0.280 Angle : 0.678 13.726 27136 Z= 0.341 Chirality : 0.042 0.276 3065 Planarity : 0.004 0.057 3416 Dihedral : 6.069 81.875 2642 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 2.72 % Allowed : 19.46 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.17), residues: 2411 helix: 1.26 (0.14), residues: 1351 sheet: -0.70 (0.36), residues: 192 loop : -1.06 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2084 HIS 0.008 0.001 HIS A3517 PHE 0.023 0.002 PHE A3611 TYR 0.017 0.001 TYR A3679 ARG 0.004 0.000 ARG A2788 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 238 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1704 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8937 (mt-10) REVERT: A 1992 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6996 (tptt) REVERT: A 2157 ASP cc_start: 0.7483 (p0) cc_final: 0.7261 (p0) REVERT: A 2213 LEU cc_start: 0.8596 (tp) cc_final: 0.8183 (mp) REVERT: A 2496 LYS cc_start: 0.9213 (tptp) cc_final: 0.8579 (pttm) REVERT: A 2756 MET cc_start: 0.8866 (tpp) cc_final: 0.8320 (ttt) REVERT: A 2871 GLN cc_start: 0.8997 (mp10) cc_final: 0.8729 (mp10) REVERT: A 3013 ASN cc_start: 0.9490 (t0) cc_final: 0.9066 (t0) REVERT: A 3015 ARG cc_start: 0.9066 (ttp-170) cc_final: 0.8684 (ttp80) REVERT: A 3313 PHE cc_start: 0.8990 (t80) cc_final: 0.8498 (t80) REVERT: A 3330 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8729 (t80) REVERT: A 3414 MET cc_start: 0.8778 (mmp) cc_final: 0.8503 (mmm) REVERT: A 3538 ASN cc_start: 0.9033 (t0) cc_final: 0.8014 (p0) REVERT: A 3540 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8478 (pm20) REVERT: A 3541 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7575 (mmm) REVERT: A 3702 MET cc_start: 0.9009 (mmm) cc_final: 0.8458 (mmm) REVERT: A 3717 GLU cc_start: 0.9201 (tp30) cc_final: 0.8653 (pp20) REVERT: A 3768 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.6222 (m-10) REVERT: A 3910 LEU cc_start: 0.9467 (mp) cc_final: 0.9235 (mp) outliers start: 60 outliers final: 49 residues processed: 279 average time/residue: 0.3102 time to fit residues: 136.4088 Evaluate side-chains 286 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 233 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1560 LYS Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1589 VAL Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 ASN Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2603 CYS Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2711 ASP Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2860 THR Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2959 GLN Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3368 ASP Chi-restraints excluded: chain A residue 3487 ASP Chi-restraints excluded: chain A residue 3491 ASP Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3541 MET Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3803 LEU Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 205 optimal weight: 30.0000 chunk 216 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20062 Z= 0.219 Angle : 0.665 15.242 27136 Z= 0.330 Chirality : 0.042 0.356 3065 Planarity : 0.004 0.056 3416 Dihedral : 5.956 81.657 2642 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.77 % Allowed : 19.87 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.17), residues: 2411 helix: 1.41 (0.14), residues: 1341 sheet: -0.71 (0.36), residues: 193 loop : -0.99 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1607 HIS 0.007 0.001 HIS A3517 PHE 0.033 0.002 PHE A1491 TYR 0.027 0.001 TYR A3369 ARG 0.004 0.000 ARG A2586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 251 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1415 MET cc_start: 0.8719 (mtt) cc_final: 0.8481 (ptp) REVERT: A 1704 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8913 (mt-10) REVERT: A 2157 ASP cc_start: 0.7470 (p0) cc_final: 0.7254 (p0) REVERT: A 2213 LEU cc_start: 0.8565 (tp) cc_final: 0.8168 (mp) REVERT: A 2496 LYS cc_start: 0.9208 (tptp) cc_final: 0.8592 (pttm) REVERT: A 2756 MET cc_start: 0.8825 (tpp) cc_final: 0.8266 (ttt) REVERT: A 2792 LEU cc_start: 0.9228 (mt) cc_final: 0.8652 (mp) REVERT: A 2871 GLN cc_start: 0.8977 (mp10) cc_final: 0.8703 (mp10) REVERT: A 3013 ASN cc_start: 0.9456 (t0) cc_final: 0.9055 (t0) REVERT: A 3015 ARG cc_start: 0.9065 (ttp-170) cc_final: 0.8674 (ttp80) REVERT: A 3311 LYS cc_start: 0.9176 (tmmt) cc_final: 0.8858 (tmmt) REVERT: A 3313 PHE cc_start: 0.9008 (t80) cc_final: 0.8521 (t80) REVERT: A 3330 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8756 (t80) REVERT: A 3414 MET cc_start: 0.8771 (mmp) cc_final: 0.8503 (mmm) REVERT: A 3538 ASN cc_start: 0.9017 (t0) cc_final: 0.7979 (p0) REVERT: A 3540 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8487 (pm20) REVERT: A 3541 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7594 (mmm) REVERT: A 3616 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6830 (pm20) REVERT: A 3655 ARG cc_start: 0.8945 (ttm110) cc_final: 0.8578 (mtp85) REVERT: A 3702 MET cc_start: 0.9004 (mmm) cc_final: 0.8478 (mmm) REVERT: A 3717 GLU cc_start: 0.9182 (tp30) cc_final: 0.8640 (pp20) REVERT: A 3768 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6276 (m-10) REVERT: A 3910 LEU cc_start: 0.9449 (mp) cc_final: 0.9213 (mp) outliers start: 61 outliers final: 45 residues processed: 295 average time/residue: 0.3001 time to fit residues: 140.3251 Evaluate side-chains 288 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 239 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1560 LYS Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2155 ASP Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2173 ASN Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2257 PHE Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2860 THR Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3368 ASP Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3487 ASP Chi-restraints excluded: chain A residue 3491 ASP Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3541 MET Chi-restraints excluded: chain A residue 3616 GLU Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3803 LEU Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 4024 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 chunk 221 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2173 ASN ** A3648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20062 Z= 0.230 Angle : 0.683 15.502 27136 Z= 0.337 Chirality : 0.042 0.292 3065 Planarity : 0.004 0.055 3416 Dihedral : 5.929 81.506 2642 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 2.27 % Allowed : 20.60 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.17), residues: 2411 helix: 1.36 (0.14), residues: 1345 sheet: -0.70 (0.36), residues: 193 loop : -1.05 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2084 HIS 0.007 0.001 HIS A3517 PHE 0.030 0.002 PHE A1491 TYR 0.025 0.001 TYR A3369 ARG 0.004 0.000 ARG A2586 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4822 Ramachandran restraints generated. 2411 Oldfield, 0 Emsley, 2411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 242 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1415 MET cc_start: 0.8749 (mtt) cc_final: 0.8506 (ptp) REVERT: A 1704 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8908 (mt-10) REVERT: A 2157 ASP cc_start: 0.7505 (p0) cc_final: 0.7290 (p0) REVERT: A 2213 LEU cc_start: 0.8581 (tp) cc_final: 0.8169 (mp) REVERT: A 2496 LYS cc_start: 0.9209 (tptp) cc_final: 0.8597 (pttm) REVERT: A 2756 MET cc_start: 0.8857 (tpp) cc_final: 0.8310 (ttt) REVERT: A 2792 LEU cc_start: 0.9237 (mt) cc_final: 0.8960 (mp) REVERT: A 2871 GLN cc_start: 0.8976 (mp10) cc_final: 0.8699 (mp10) REVERT: A 3013 ASN cc_start: 0.9449 (t0) cc_final: 0.9059 (t0) REVERT: A 3015 ARG cc_start: 0.9054 (ttp-170) cc_final: 0.8663 (ttp80) REVERT: A 3313 PHE cc_start: 0.9024 (t80) cc_final: 0.8520 (t80) REVERT: A 3330 TYR cc_start: 0.9200 (OUTLIER) cc_final: 0.8756 (t80) REVERT: A 3414 MET cc_start: 0.8800 (mmp) cc_final: 0.8504 (mmm) REVERT: A 3538 ASN cc_start: 0.9027 (t0) cc_final: 0.7984 (p0) REVERT: A 3540 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8478 (pm20) REVERT: A 3541 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7608 (mmm) REVERT: A 3616 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6834 (pm20) REVERT: A 3655 ARG cc_start: 0.8961 (ttm110) cc_final: 0.8596 (mtp85) REVERT: A 3702 MET cc_start: 0.9009 (mmm) cc_final: 0.8580 (mmm) REVERT: A 3717 GLU cc_start: 0.9184 (tp30) cc_final: 0.8641 (pp20) REVERT: A 3768 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.6295 (m-10) REVERT: A 3910 LEU cc_start: 0.9450 (mp) cc_final: 0.9212 (mp) outliers start: 50 outliers final: 43 residues processed: 277 average time/residue: 0.3258 time to fit residues: 141.3910 Evaluate side-chains 281 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 234 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1558 VAL Chi-restraints excluded: chain A residue 1560 LYS Chi-restraints excluded: chain A residue 1578 PHE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1592 LEU Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1992 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2155 ASP Chi-restraints excluded: chain A residue 2171 ASP Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2378 VAL Chi-restraints excluded: chain A residue 2439 ASP Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2494 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2794 ASP Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2860 THR Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3321 ILE Chi-restraints excluded: chain A residue 3328 SER Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3487 ASP Chi-restraints excluded: chain A residue 3491 ASP Chi-restraints excluded: chain A residue 3505 ILE Chi-restraints excluded: chain A residue 3541 MET Chi-restraints excluded: chain A residue 3616 GLU Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3737 THR Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3768 PHE Chi-restraints excluded: chain A residue 3803 LEU Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 192 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 168 optimal weight: 6.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.087615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066194 restraints weight = 81292.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.068151 restraints weight = 46356.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069476 restraints weight = 32151.971| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20062 Z= 0.206 Angle : 0.681 15.748 27136 Z= 0.335 Chirality : 0.042 0.285 3065 Planarity : 0.004 0.055 3416 Dihedral : 5.859 81.961 2642 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 2.45 % Allowed : 20.69 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.17), residues: 2411 helix: 1.41 (0.14), residues: 1345 sheet: -0.71 (0.36), residues: 193 loop : -1.00 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A2125 HIS 0.007 0.001 HIS A3517 PHE 0.066 0.002 PHE A3703 TYR 0.025 0.001 TYR A3369 ARG 0.005 0.000 ARG A2586 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5593.00 seconds wall clock time: 101 minutes 49.08 seconds (6109.08 seconds total)