Starting phenix.real_space_refine on Sat Mar 23 02:38:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tay_10430/03_2024/6tay_10430_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tay_10430/03_2024/6tay_10430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tay_10430/03_2024/6tay_10430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tay_10430/03_2024/6tay_10430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tay_10430/03_2024/6tay_10430_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tay_10430/03_2024/6tay_10430_neut_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 208 5.16 5 C 22441 2.51 5 N 6059 2.21 5 O 6527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2507": "NH1" <-> "NH2" Residue "A ARG 2523": "NH1" <-> "NH2" Residue "A PHE 2637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3479": "NH1" <-> "NH2" Residue "A ARG 3591": "NH1" <-> "NH2" Residue "A PHE 4607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4924": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35241 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 35241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4421, 35241 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'peptide': 4417, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 181, 'TRANS': 4235, None: 4} Not linked: pdbres="GLY A5150 " pdbres="ATP A5201 " Not linked: pdbres="ATP A5201 " pdbres=" MG A5202 " Not linked: pdbres=" MG A5202 " pdbres=" ZN A5203 " Not linked: pdbres=" ZN A5203 " pdbres=" ZN A5204 " Chain breaks: 15 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'UNK:plan-1': 67, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26230 SG CYS A3962 88.596 133.489 219.905 1.00121.06 S ATOM 26394 SG CYS A3982 86.094 131.351 222.600 1.00124.67 S ATOM 26419 SG CYS A3985 89.737 131.777 222.863 1.00127.04 S ATOM 26120 SG CYS A3947 79.329 126.208 217.232 0.50 96.21 S ATOM 26145 SG CYS A3950 76.707 123.355 216.016 1.00104.83 S ATOM 26273 SG CYS A3967 76.780 126.459 214.111 1.00111.70 S ATOM 26298 SG CYS A3970 75.210 126.926 217.834 1.00115.80 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N CYS A3947 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS A3947 " occ=0.50 Time building chain proxies: 17.61, per 1000 atoms: 0.50 Number of scatterers: 35241 At special positions: 0 Unit cell: (128.96, 153.92, 243.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 208 16.00 P 3 15.00 Mg 1 11.99 O 6527 8.00 N 6059 7.00 C 22441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 992 " distance=2.03 Simple disulfide: pdb=" SG CYS A2605 " - pdb=" SG CYS A2653 " distance=2.04 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: 13.00 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5203 " pdb="ZN ZN A5203 " - pdb=" ND1 HIS A3964 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3982 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3962 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3985 " pdb=" ZN A5204 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3967 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3970 " Number of angles added : 9 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 205 helices and 14 sheets defined 54.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 21.45 Creating SS restraints... Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.928A pdb=" N UNK A 522 " --> pdb=" O UNK A 518 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N UNK A 523 " --> pdb=" O UNK A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 604 removed outlier: 5.444A pdb=" N ALA A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 619 removed outlier: 4.390A pdb=" N LYS A 612 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 617 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS A 618 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 644 through 655 Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 700 through 703 No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 721 through 725 removed outlier: 3.565A pdb=" N ARG A 725 " --> pdb=" O ALA A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 749 removed outlier: 5.511A pdb=" N SER A 744 " --> pdb=" O GLU A 741 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 745 " --> pdb=" O SER A 742 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 749 " --> pdb=" O TYR A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 removed outlier: 3.826A pdb=" N ASP A 756 " --> pdb=" O ASP A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'A' and resid 781 through 800 Processing helix chain 'A' and resid 811 through 827 Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.780A pdb=" N ILE A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 888 Processing helix chain 'A' and resid 908 through 916 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.618A pdb=" N GLN A 940 " --> pdb=" O GLY A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 963 through 981 Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'A' and resid 1021 through 1030 Processing helix chain 'A' and resid 1033 through 1042 Processing helix chain 'A' and resid 1048 through 1050 No H-bonds generated for 'chain 'A' and resid 1048 through 1050' Processing helix chain 'A' and resid 1053 through 1069 Processing helix chain 'A' and resid 1080 through 1087 Processing helix chain 'A' and resid 1090 through 1102 Processing helix chain 'A' and resid 1114 through 1142 Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1167 through 1170 Processing helix chain 'A' and resid 1191 through 1201 Processing helix chain 'A' and resid 1207 through 1218 Processing helix chain 'A' and resid 1234 through 1240 removed outlier: 3.808A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1258 removed outlier: 4.038A pdb=" N SER A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1272 removed outlier: 4.797A pdb=" N LYS A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP A1272 " --> pdb=" O ALA A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1288 Processing helix chain 'A' and resid 1299 through 1329 Processing helix chain 'A' and resid 1339 through 1343 Processing helix chain 'A' and resid 1362 through 1369 removed outlier: 3.797A pdb=" N ALA A1366 " --> pdb=" O GLN A1362 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A1369 " --> pdb=" O LYS A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1386 Processing helix chain 'A' and resid 1388 through 1397 Processing helix chain 'A' and resid 1404 through 1414 removed outlier: 3.880A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1434 removed outlier: 3.663A pdb=" N ASP A1423 " --> pdb=" O ASP A1419 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1462 removed outlier: 4.012A pdb=" N GLU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1484 removed outlier: 3.587A pdb=" N LEU A1479 " --> pdb=" O SER A1475 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU A1480 " --> pdb=" O ALA A1476 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP A1481 " --> pdb=" O ARG A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1506 Processing helix chain 'A' and resid 1522 through 1525 No H-bonds generated for 'chain 'A' and resid 1522 through 1525' Processing helix chain 'A' and resid 1545 through 1556 Processing helix chain 'A' and resid 1564 through 1593 Processing helix chain 'A' and resid 1631 through 1659 Processing helix chain 'A' and resid 1662 through 1664 No H-bonds generated for 'chain 'A' and resid 1662 through 1664' Processing helix chain 'A' and resid 1668 through 1678 Processing helix chain 'A' and resid 1685 through 1693 removed outlier: 4.476A pdb=" N PHE A1693 " --> pdb=" O MET A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1700 through 1708 Processing helix chain 'A' and resid 1713 through 1731 Proline residue: A1727 - end of helix Processing helix chain 'A' and resid 1736 through 1749 Processing helix chain 'A' and resid 1761 through 1771 Processing helix chain 'A' and resid 1802 through 1809 Processing helix chain 'A' and resid 1833 through 1843 Processing helix chain 'A' and resid 1864 through 1879 Processing helix chain 'A' and resid 1894 through 1896 No H-bonds generated for 'chain 'A' and resid 1894 through 1896' Processing helix chain 'A' and resid 1900 through 1908 removed outlier: 6.246A pdb=" N GLN A1907 " --> pdb=" O SER A1903 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR A1908 " --> pdb=" O THR A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1918 through 1929 Processing helix chain 'A' and resid 1939 through 1941 No H-bonds generated for 'chain 'A' and resid 1939 through 1941' Processing helix chain 'A' and resid 1960 through 1974 Processing helix chain 'A' and resid 1994 through 2005 Proline residue: A2003 - end of helix Processing helix chain 'A' and resid 2028 through 2036 Processing helix chain 'A' and resid 2082 through 2087 removed outlier: 3.548A pdb=" N ASP A2086 " --> pdb=" O PHE A2082 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A2087 " --> pdb=" O LYS A2083 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2082 through 2087' Processing helix chain 'A' and resid 2096 through 2100 removed outlier: 3.853A pdb=" N ILE A2100 " --> pdb=" O PRO A2096 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2096 through 2100' Processing helix chain 'A' and resid 2117 through 2120 No H-bonds generated for 'chain 'A' and resid 2117 through 2120' Processing helix chain 'A' and resid 2127 through 2136 removed outlier: 4.042A pdb=" N ARG A2134 " --> pdb=" O GLN A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2165 removed outlier: 3.839A pdb=" N TYR A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2173 through 2191 Processing helix chain 'A' and resid 2195 through 2202 Processing helix chain 'A' and resid 2208 through 2223 Processing helix chain 'A' and resid 2309 through 2317 Processing helix chain 'A' and resid 2331 through 2341 Processing helix chain 'A' and resid 2358 through 2373 Processing helix chain 'A' and resid 2387 through 2399 Processing helix chain 'A' and resid 2418 through 2439 Processing helix chain 'A' and resid 2456 through 2463 Processing helix chain 'A' and resid 2493 through 2501 removed outlier: 3.772A pdb=" N SER A2501 " --> pdb=" O LEU A2497 " (cutoff:3.500A) Processing helix chain 'A' and resid 2537 through 2539 No H-bonds generated for 'chain 'A' and resid 2537 through 2539' Processing helix chain 'A' and resid 2549 through 2562 removed outlier: 5.008A pdb=" N TYR A2554 " --> pdb=" O ALA A2550 " (cutoff:3.500A) Processing helix chain 'A' and resid 2570 through 2589 removed outlier: 3.529A pdb=" N LYS A2589 " --> pdb=" O MET A2585 " (cutoff:3.500A) Processing helix chain 'A' and resid 2599 through 2614 Processing helix chain 'A' and resid 2619 through 2630 Processing helix chain 'A' and resid 2643 through 2653 Processing helix chain 'A' and resid 2661 through 2668 Processing helix chain 'A' and resid 2674 through 2676 No H-bonds generated for 'chain 'A' and resid 2674 through 2676' Processing helix chain 'A' and resid 2679 through 2695 Processing helix chain 'A' and resid 2707 through 2721 Processing helix chain 'A' and resid 2738 through 2746 Processing helix chain 'A' and resid 2755 through 2758 No H-bonds generated for 'chain 'A' and resid 2755 through 2758' Processing helix chain 'A' and resid 2776 through 2790 removed outlier: 3.530A pdb=" N ILE A2780 " --> pdb=" O PRO A2776 " (cutoff:3.500A) Processing helix chain 'A' and resid 2818 through 2826 removed outlier: 4.049A pdb=" N HIS A2822 " --> pdb=" O LYS A2819 " (cutoff:3.500A) Proline residue: A2823 - end of helix removed outlier: 3.740A pdb=" N GLU A2826 " --> pdb=" O PRO A2823 " (cutoff:3.500A) Processing helix chain 'A' and resid 2852 through 2855 No H-bonds generated for 'chain 'A' and resid 2852 through 2855' Processing helix chain 'A' and resid 2868 through 2881 removed outlier: 5.317A pdb=" N SER A2881 " --> pdb=" O GLY A2877 " (cutoff:3.500A) Processing helix chain 'A' and resid 2883 through 2906 removed outlier: 5.723A pdb=" N GLY A2891 " --> pdb=" O ASP A2887 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR A2892 " --> pdb=" O LYS A2888 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A2893 " --> pdb=" O ILE A2889 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA A2894 " --> pdb=" O ARG A2890 " (cutoff:3.500A) Proline residue: A2895 - end of helix Processing helix chain 'A' and resid 2914 through 2931 Processing helix chain 'A' and resid 2937 through 2947 Processing helix chain 'A' and resid 2956 through 2963 removed outlier: 3.791A pdb=" N SER A2963 " --> pdb=" O ILE A2959 " (cutoff:3.500A) Processing helix chain 'A' and resid 2975 through 2983 Processing helix chain 'A' and resid 3011 through 3018 Processing helix chain 'A' and resid 3038 through 3055 Processing helix chain 'A' and resid 3064 through 3067 No H-bonds generated for 'chain 'A' and resid 3064 through 3067' Processing helix chain 'A' and resid 3072 through 3075 No H-bonds generated for 'chain 'A' and resid 3072 through 3075' Processing helix chain 'A' and resid 3113 through 3118 Processing helix chain 'A' and resid 3122 through 3127 removed outlier: 3.901A pdb=" N ARG A3127 " --> pdb=" O PRO A3123 " (cutoff:3.500A) Processing helix chain 'A' and resid 3141 through 3158 Processing helix chain 'A' and resid 3173 through 3176 No H-bonds generated for 'chain 'A' and resid 3173 through 3176' Processing helix chain 'A' and resid 3186 through 3196 Processing helix chain 'A' and resid 3204 through 3220 removed outlier: 3.881A pdb=" N LYS A3208 " --> pdb=" O GLU A3204 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A3220 " --> pdb=" O ILE A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3223 through 3231 removed outlier: 4.709A pdb=" N SER A3230 " --> pdb=" O VAL A3226 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLY A3231 " --> pdb=" O VAL A3227 " (cutoff:3.500A) Processing helix chain 'A' and resid 3235 through 3247 Processing helix chain 'A' and resid 3255 through 3263 Processing helix chain 'A' and resid 3287 through 3295 Processing helix chain 'A' and resid 3308 through 3310 No H-bonds generated for 'chain 'A' and resid 3308 through 3310' Processing helix chain 'A' and resid 3314 through 3325 Processing helix chain 'A' and resid 3350 through 3364 Processing helix chain 'A' and resid 3384 through 3387 No H-bonds generated for 'chain 'A' and resid 3384 through 3387' Processing helix chain 'A' and resid 3416 through 3419 No H-bonds generated for 'chain 'A' and resid 3416 through 3419' Processing helix chain 'A' and resid 3423 through 3426 Processing helix chain 'A' and resid 3477 through 3491 removed outlier: 4.935A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET A3491 " --> pdb=" O GLY A3487 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3512 Processing helix chain 'A' and resid 3519 through 3541 removed outlier: 4.280A pdb=" N ASN A3541 " --> pdb=" O LYS A3537 " (cutoff:3.500A) Processing helix chain 'A' and resid 3544 through 3547 No H-bonds generated for 'chain 'A' and resid 3544 through 3547' Processing helix chain 'A' and resid 3549 through 3554 Processing helix chain 'A' and resid 3557 through 3563 Processing helix chain 'A' and resid 3566 through 3589 Proline residue: A3580 - end of helix removed outlier: 3.895A pdb=" N HIS A3588 " --> pdb=" O SER A3584 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3615 Processing helix chain 'A' and resid 3658 through 3675 Processing helix chain 'A' and resid 3681 through 3690 Processing helix chain 'A' and resid 3693 through 3700 removed outlier: 3.748A pdb=" N GLN A3700 " --> pdb=" O VAL A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3703 through 3721 removed outlier: 3.601A pdb=" N LYS A3708 " --> pdb=" O ALA A3704 " (cutoff:3.500A) Processing helix chain 'A' and resid 3728 through 3746 removed outlier: 3.599A pdb=" N GLU A3746 " --> pdb=" O ARG A3742 " (cutoff:3.500A) Processing helix chain 'A' and resid 3761 through 3770 removed outlier: 3.512A pdb=" N LEU A3766 " --> pdb=" O TRP A3763 " (cutoff:3.500A) Processing helix chain 'A' and resid 3772 through 3784 Processing helix chain 'A' and resid 3786 through 3799 removed outlier: 3.897A pdb=" N SER A3790 " --> pdb=" O GLN A3787 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA A3796 " --> pdb=" O SER A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3808 through 3822 Processing helix chain 'A' and resid 3829 through 3838 removed outlier: 3.914A pdb=" N LEU A3833 " --> pdb=" O PRO A3829 " (cutoff:3.500A) Processing helix chain 'A' and resid 3840 through 3846 Processing helix chain 'A' and resid 3857 through 3889 removed outlier: 4.588A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY A3886 " --> pdb=" O HIS A3882 " (cutoff:3.500A) Processing helix chain 'A' and resid 3895 through 3909 removed outlier: 3.542A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3918 through 3940 Processing helix chain 'A' and resid 3968 through 3974 Processing helix chain 'A' and resid 4001 through 4025 Processing helix chain 'A' and resid 4036 through 4045 Processing helix chain 'A' and resid 4083 through 4088 Processing helix chain 'A' and resid 4093 through 4095 No H-bonds generated for 'chain 'A' and resid 4093 through 4095' Processing helix chain 'A' and resid 4097 through 4110 Processing helix chain 'A' and resid 4118 through 4137 Processing helix chain 'A' and resid 4143 through 4156 removed outlier: 3.692A pdb=" N THR A4156 " --> pdb=" O HIS A4152 " (cutoff:3.500A) Processing helix chain 'A' and resid 4172 through 4195 removed outlier: 3.759A pdb=" N GLU A4194 " --> pdb=" O ASP A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4204 through 4218 Processing helix chain 'A' and resid 4223 through 4235 Processing helix chain 'A' and resid 4238 through 4244 removed outlier: 3.784A pdb=" N PHE A4244 " --> pdb=" O PHE A4240 " (cutoff:3.500A) Processing helix chain 'A' and resid 4252 through 4254 No H-bonds generated for 'chain 'A' and resid 4252 through 4254' Processing helix chain 'A' and resid 4259 through 4262 No H-bonds generated for 'chain 'A' and resid 4259 through 4262' Processing helix chain 'A' and resid 4280 through 4292 Processing helix chain 'A' and resid 4298 through 4304 Processing helix chain 'A' and resid 4310 through 4330 Processing helix chain 'A' and resid 4343 through 4352 Processing helix chain 'A' and resid 4354 through 4356 No H-bonds generated for 'chain 'A' and resid 4354 through 4356' Processing helix chain 'A' and resid 4362 through 4369 Processing helix chain 'A' and resid 4385 through 4402 Processing helix chain 'A' and resid 4409 through 4415 Processing helix chain 'A' and resid 4523 through 4543 removed outlier: 3.648A pdb=" N HIS A4543 " --> pdb=" O VAL A4539 " (cutoff:3.500A) Processing helix chain 'A' and resid 4545 through 4551 Processing helix chain 'A' and resid 4560 through 4577 Processing helix chain 'A' and resid 4582 through 4596 Processing helix chain 'A' and resid 4614 through 4632 Processing helix chain 'A' and resid 4635 through 4647 Proline residue: A4640 - end of helix Processing helix chain 'A' and resid 4656 through 4659 No H-bonds generated for 'chain 'A' and resid 4656 through 4659' Processing helix chain 'A' and resid 4666 through 4668 No H-bonds generated for 'chain 'A' and resid 4666 through 4668' Processing helix chain 'A' and resid 4692 through 4701 Processing helix chain 'A' and resid 4704 through 4707 No H-bonds generated for 'chain 'A' and resid 4704 through 4707' Processing helix chain 'A' and resid 4709 through 4716 Processing helix chain 'A' and resid 4718 through 4721 No H-bonds generated for 'chain 'A' and resid 4718 through 4721' Processing helix chain 'A' and resid 4724 through 4740 Proline residue: A4728 - end of helix removed outlier: 3.510A pdb=" N LEU A4731 " --> pdb=" O PRO A4728 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A4735 " --> pdb=" O ALA A4732 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A4738 " --> pdb=" O ARG A4735 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4756 Processing helix chain 'A' and resid 4762 through 4782 Processing helix chain 'A' and resid 4785 through 4788 No H-bonds generated for 'chain 'A' and resid 4785 through 4788' Processing helix chain 'A' and resid 4809 through 4812 removed outlier: 3.501A pdb=" N ILE A4812 " --> pdb=" O PHE A4809 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4809 through 4812' Processing helix chain 'A' and resid 4821 through 4844 Processing helix chain 'A' and resid 4855 through 4857 No H-bonds generated for 'chain 'A' and resid 4855 through 4857' Processing helix chain 'A' and resid 4872 through 4879 removed outlier: 3.958A pdb=" N ASN A4879 " --> pdb=" O LEU A4875 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4906 Processing helix chain 'A' and resid 4930 through 4940 Processing helix chain 'A' and resid 4948 through 4957 removed outlier: 3.638A pdb=" N SER A4952 " --> pdb=" O ASN A4948 " (cutoff:3.500A) Processing helix chain 'A' and resid 4961 through 4979 Processing helix chain 'A' and resid 5004 through 5012 removed outlier: 4.996A pdb=" N ARG A5012 " --> pdb=" O LYS A5008 " (cutoff:3.500A) Processing helix chain 'A' and resid 5019 through 5035 Processing helix chain 'A' and resid 5054 through 5065 Processing helix chain 'A' and resid 5069 through 5083 removed outlier: 4.070A pdb=" N LEU A5074 " --> pdb=" O ASP A5070 " (cutoff:3.500A) Processing helix chain 'A' and resid 5099 through 5109 Processing helix chain 'A' and resid 5114 through 5116 No H-bonds generated for 'chain 'A' and resid 5114 through 5116' Processing helix chain 'A' and resid 5118 through 5121 Processing helix chain 'A' and resid 5128 through 5148 removed outlier: 3.710A pdb=" N CYS A5131 " --> pdb=" O MET A5128 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE A5132 " --> pdb=" O SER A5129 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A5133 " --> pdb=" O SER A5130 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A5138 " --> pdb=" O TRP A5135 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A5146 " --> pdb=" O TRP A5143 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A5147 " --> pdb=" O ASP A5144 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A5148 " --> pdb=" O ARG A5145 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 1149 through 1151 Processing sheet with id= B, first strand: chain 'A' and resid 1625 through 1627 removed outlier: 3.758A pdb=" N GLY A1612 " --> pdb=" O TYR A1606 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1792 through 1796 removed outlier: 7.094A pdb=" N LEU A1888 " --> pdb=" O ASN A1793 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A1795 " --> pdb=" O LEU A1888 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A1890 " --> pdb=" O ILE A1795 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 7.793A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A2057 " --> pdb=" O GLY A1949 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A1951 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A2059 " --> pdb=" O VAL A1951 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER A1953 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE A2061 " --> pdb=" O SER A1953 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N HIS A2017 " --> pdb=" O PRO A1981 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS A1983 " --> pdb=" O HIS A2017 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A2019 " --> pdb=" O LYS A1983 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A1985 " --> pdb=" O ASP A2019 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id= F, first strand: chain 'A' and resid 2266 through 2269 Processing sheet with id= G, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id= H, first strand: chain 'A' and resid 2540 through 2542 removed outlier: 7.096A pdb=" N ILE A2378 " --> pdb=" O TRP A2541 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A2377 " --> pdb=" O ILE A2481 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2859 through 2862 removed outlier: 6.035A pdb=" N GLN A2762 " --> pdb=" O VAL A2799 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A2801 " --> pdb=" O GLN A2762 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS A2764 " --> pdb=" O VAL A2801 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A2803 " --> pdb=" O HIS A2764 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A2766 " --> pdb=" O VAL A2803 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 3130 through 3132 removed outlier: 6.060A pdb=" N LEU A3003 " --> pdb=" O HIS A3131 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A3059 " --> pdb=" O ILE A3108 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE A3110 " --> pdb=" O VAL A3059 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU A3061 " --> pdb=" O ILE A3110 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLU A3112 " --> pdb=" O LEU A3061 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU A3026 " --> pdb=" O VAL A3060 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 3080 through 3082 removed outlier: 4.541A pdb=" N LYS A3086 " --> pdb=" O VAL A3101 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 3396 through 3400 removed outlier: 9.316A pdb=" N ARG A3397 " --> pdb=" O ALA A3272 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE A3274 " --> pdb=" O ARG A3397 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL A3399 " --> pdb=" O PHE A3274 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU A3276 " --> pdb=" O VAL A3399 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A3371 " --> pdb=" O VAL A3273 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N THR A3275 " --> pdb=" O VAL A3371 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A3373 " --> pdb=" O THR A3275 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE A3277 " --> pdb=" O VAL A3373 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE A3375 " --> pdb=" O ILE A3277 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR A3279 " --> pdb=" O PHE A3375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A3377 " --> pdb=" O THR A3279 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS A3332 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N TYR A3374 " --> pdb=" O LYS A3332 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A3304 " --> pdb=" O VAL A3335 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLN A3337 " --> pdb=" O VAL A3304 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU A3306 " --> pdb=" O GLN A3337 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASP A3339 " --> pdb=" O LEU A3306 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 3957 through 3959 Processing sheet with id= N, first strand: chain 'A' and resid 4880 through 4883 1540 hydrogen bonds defined for protein. 4440 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: 21.67 Time building geometry restraints manager: 14.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11182 1.34 - 1.46: 7801 1.46 - 1.58: 16668 1.58 - 1.70: 5 1.70 - 1.83: 305 Bond restraints: 35961 Sorted by residual: bond pdb=" C4 ATP A5201 " pdb=" C5 ATP A5201 " ideal model delta sigma weight residual 1.388 1.449 -0.061 1.00e-02 1.00e+04 3.77e+01 bond pdb=" C5 ATP A5201 " pdb=" N7 ATP A5201 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.66e+01 bond pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 1.374 1.316 0.058 1.00e-02 1.00e+04 3.38e+01 bond pdb=" C5 ATP A5201 " pdb=" C6 ATP A5201 " ideal model delta sigma weight residual 1.409 1.460 -0.051 1.00e-02 1.00e+04 2.58e+01 bond pdb=" C4' ATP A5201 " pdb=" O4' ATP A5201 " ideal model delta sigma weight residual 1.444 1.401 0.043 1.10e-02 8.26e+03 1.51e+01 ... (remaining 35956 not shown) Histogram of bond angle deviations from ideal: 94.88 - 103.01: 239 103.01 - 111.14: 13554 111.14 - 119.27: 16731 119.27 - 127.40: 17731 127.40 - 135.53: 415 Bond angle restraints: 48670 Sorted by residual: angle pdb=" PB ATP A5201 " pdb=" O3B ATP A5201 " pdb=" PG ATP A5201 " ideal model delta sigma weight residual 139.87 122.62 17.25 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PA ATP A5201 " pdb=" O3A ATP A5201 " pdb=" PB ATP A5201 " ideal model delta sigma weight residual 136.83 124.15 12.68 1.00e+00 1.00e+00 1.61e+02 angle pdb=" C5 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N3 ATP A5201 " ideal model delta sigma weight residual 126.80 118.87 7.93 1.00e+00 1.00e+00 6.28e+01 angle pdb=" N3 ATP A5201 " pdb=" C4 ATP A5201 " pdb=" N9 ATP A5201 " ideal model delta sigma weight residual 127.04 135.53 -8.49 1.15e+00 7.59e-01 5.47e+01 angle pdb=" N VAL A 759 " pdb=" CA VAL A 759 " pdb=" C VAL A 759 " ideal model delta sigma weight residual 113.20 106.79 6.41 9.60e-01 1.09e+00 4.45e+01 ... (remaining 48665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 20598 16.85 - 33.70: 1056 33.70 - 50.54: 212 50.54 - 67.39: 18 67.39 - 84.24: 33 Dihedral angle restraints: 21917 sinusoidal: 8928 harmonic: 12989 Sorted by residual: dihedral pdb=" CA ILE A1373 " pdb=" C ILE A1373 " pdb=" N SER A1374 " pdb=" CA SER A1374 " ideal model delta harmonic sigma weight residual 180.00 129.84 50.16 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA THR A2225 " pdb=" C THR A2225 " pdb=" N PRO A2226 " pdb=" CA PRO A2226 " ideal model delta harmonic sigma weight residual 180.00 147.68 32.32 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA SER A 779 " pdb=" C SER A 779 " pdb=" N ASN A 780 " pdb=" CA ASN A 780 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 ... (remaining 21914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4342 0.074 - 0.147: 1016 0.147 - 0.221: 129 0.221 - 0.295: 16 0.295 - 0.368: 9 Chirality restraints: 5512 Sorted by residual: chirality pdb=" CB ILE A 896 " pdb=" CA ILE A 896 " pdb=" CG1 ILE A 896 " pdb=" CG2 ILE A 896 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB VAL A3010 " pdb=" CA VAL A3010 " pdb=" CG1 VAL A3010 " pdb=" CG2 VAL A3010 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE A2378 " pdb=" CA ILE A2378 " pdb=" CG1 ILE A2378 " pdb=" CG2 ILE A2378 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 5509 not shown) Planarity restraints: 6228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A2783 " -0.023 2.00e-02 2.50e+03 2.75e-02 1.32e+01 pdb=" CG PHE A2783 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A2783 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A2783 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A2783 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A2783 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A2783 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2960 " -0.024 2.00e-02 2.50e+03 2.68e-02 1.25e+01 pdb=" CG PHE A2960 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A2960 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A2960 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A2960 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A2960 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A2960 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A4323 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR A4323 " 0.059 2.00e-02 2.50e+03 pdb=" O THR A4323 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU A4324 " -0.020 2.00e-02 2.50e+03 ... (remaining 6225 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 375 2.63 - 3.20: 31185 3.20 - 3.77: 55776 3.77 - 4.33: 77142 4.33 - 4.90: 125589 Nonbonded interactions: 290067 Sorted by model distance: nonbonded pdb=" OE2 GLU A2060 " pdb="MG MG A5202 " model vdw 2.066 2.170 nonbonded pdb=" OG SER A1961 " pdb="MG MG A5202 " model vdw 2.069 2.170 nonbonded pdb=" O GLU A1375 " pdb=" NH1 ARG A1379 " model vdw 2.171 2.520 nonbonded pdb=" OH TYR A3664 " pdb=" OG1 THR A3692 " model vdw 2.233 2.440 nonbonded pdb=" O LEU A 848 " pdb=" OG SER A 852 " model vdw 2.243 2.440 ... (remaining 290062 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 10.990 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 102.180 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.150 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.011 0.143 35961 Z= 0.688 Angle : 1.154 17.247 48670 Z= 0.615 Chirality : 0.064 0.368 5512 Planarity : 0.008 0.081 6228 Dihedral : 11.357 84.238 13451 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.91 % Favored : 90.97 % Rotamer: Outliers : 0.28 % Allowed : 3.44 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.10), residues: 4320 helix: -2.17 (0.08), residues: 2444 sheet: -0.85 (0.32), residues: 241 loop : -3.01 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP A5022 HIS 0.030 0.004 HIS A2688 PHE 0.060 0.005 PHE A2960 TYR 0.051 0.004 TYR A2057 ARG 0.021 0.002 ARG A2523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 519 time to evaluate : 4.269 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: A 663 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7536 (ttm110) REVERT: A 883 ASN cc_start: 0.8284 (m-40) cc_final: 0.8075 (m-40) REVERT: A 934 MET cc_start: 0.7527 (ttp) cc_final: 0.7314 (ttm) REVERT: A 940 GLN cc_start: 0.7315 (mt0) cc_final: 0.6795 (tm-30) REVERT: A 1120 ARG cc_start: 0.7719 (mmt-90) cc_final: 0.7499 (mmt180) REVERT: A 1134 VAL cc_start: 0.8523 (t) cc_final: 0.8237 (p) REVERT: A 1305 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7434 (mt0) REVERT: A 1409 ASP cc_start: 0.7865 (m-30) cc_final: 0.7643 (m-30) REVERT: A 1433 GLN cc_start: 0.7962 (mt0) cc_final: 0.7621 (mt0) REVERT: A 1519 LYS cc_start: 0.8644 (mmpt) cc_final: 0.8358 (mmtm) REVERT: A 1864 TYR cc_start: 0.7948 (t80) cc_final: 0.7680 (t80) REVERT: A 2012 MET cc_start: 0.4243 (mpm) cc_final: 0.3405 (mmt) REVERT: A 2258 ARG cc_start: 0.6759 (pmt170) cc_final: 0.6433 (mtm110) REVERT: A 2259 TRP cc_start: 0.7742 (m100) cc_final: 0.7459 (m100) REVERT: A 2648 MET cc_start: 0.8754 (mmm) cc_final: 0.8205 (mmp) REVERT: A 3200 ASP cc_start: 0.7082 (p0) cc_final: 0.6871 (p0) REVERT: A 3537 LYS cc_start: 0.8592 (tmmt) cc_final: 0.8389 (tttp) REVERT: A 3619 LYS cc_start: 0.8722 (pmmt) cc_final: 0.8460 (ptpp) REVERT: A 3636 MET cc_start: 0.3772 (ptp) cc_final: 0.3351 (tpp) REVERT: A 3968 LEU cc_start: 0.8531 (tp) cc_final: 0.7866 (tp) REVERT: A 3980 MET cc_start: 0.8056 (tpp) cc_final: 0.7747 (tpp) REVERT: A 4001 HIS cc_start: 0.7428 (m-70) cc_final: 0.7189 (m-70) REVERT: A 4089 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8295 (mt) REVERT: A 4406 GLN cc_start: 0.7701 (tp40) cc_final: 0.7467 (tm-30) outliers start: 11 outliers final: 2 residues processed: 530 average time/residue: 0.5802 time to fit residues: 471.7275 Evaluate side-chains 339 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 336 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2741 ILE Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 4089 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 1.9990 chunk 335 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 346 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 401 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 ASN A 789 ASN A 822 HIS ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 GLN A1014 ASN A1089 HIS A1214 GLN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1343 ASN A1429 HIS A1433 GLN A1567 ASN A1581 GLN A1595 ASN A1660 HIS A1770 HIS A1812 GLN A1816 GLN A1849 GLN A1920 ASN A1930 GLN A2413 HIS A2480 HIS A2493 GLN A2822 HIS A2981 GLN A3131 HIS A3251 GLN A3337 GLN A3392 HIS A3496 ASN A3536 ASN A3568 HIS A3575 GLN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3777 ASN A3914 ASN A4001 HIS A4008 HIS A4060 HIS ** A4196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4395 HIS A4413 ASN A4500 GLN A4587 HIS A4590 HIS A4606 ASN A4648 GLN A4697 HIS A4759 HIS A4834 HIS ** A4900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4959 GLN A5002 GLN A5017 HIS A5146 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35961 Z= 0.203 Angle : 0.623 13.626 48670 Z= 0.315 Chirality : 0.041 0.214 5512 Planarity : 0.005 0.071 6228 Dihedral : 6.312 87.365 4801 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.48 % Favored : 92.45 % Rotamer: Outliers : 1.20 % Allowed : 7.08 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.12), residues: 4320 helix: -0.40 (0.10), residues: 2469 sheet: -0.43 (0.34), residues: 227 loop : -2.60 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A5022 HIS 0.009 0.001 HIS A4587 PHE 0.040 0.002 PHE A2371 TYR 0.023 0.001 TYR A1717 ARG 0.006 0.000 ARG A3345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 370 time to evaluate : 4.102 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 934 MET cc_start: 0.7420 (ttp) cc_final: 0.7212 (ttm) REVERT: A 940 GLN cc_start: 0.7331 (mt0) cc_final: 0.6801 (tm-30) REVERT: A 1120 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.7522 (mmt180) REVERT: A 1243 ASN cc_start: 0.7817 (m110) cc_final: 0.7364 (m110) REVERT: A 1377 ARG cc_start: 0.6657 (mtt180) cc_final: 0.6366 (mtt180) REVERT: A 1405 LYS cc_start: 0.8414 (mptt) cc_final: 0.8142 (mmtp) REVERT: A 1409 ASP cc_start: 0.7980 (m-30) cc_final: 0.7691 (m-30) REVERT: A 2258 ARG cc_start: 0.6805 (pmt170) cc_final: 0.6240 (ptt-90) REVERT: A 2288 ASN cc_start: 0.8388 (p0) cc_final: 0.8006 (p0) REVERT: A 2495 MET cc_start: 0.7989 (tpp) cc_final: 0.7326 (tpp) REVERT: A 2592 ASN cc_start: 0.4637 (OUTLIER) cc_final: 0.3994 (p0) REVERT: A 2648 MET cc_start: 0.8691 (mmm) cc_final: 0.8214 (mmp) REVERT: A 2977 GLU cc_start: 0.7564 (pt0) cc_final: 0.7340 (pt0) REVERT: A 3331 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7635 (mtm180) REVERT: A 3474 PHE cc_start: 0.8718 (m-10) cc_final: 0.8429 (m-10) REVERT: A 3511 ASP cc_start: 0.8089 (m-30) cc_final: 0.7802 (m-30) REVERT: A 3552 ARG cc_start: 0.7558 (tpp-160) cc_final: 0.7223 (mmp-170) REVERT: A 3619 LYS cc_start: 0.8670 (pmmt) cc_final: 0.8381 (pttm) outliers start: 47 outliers final: 17 residues processed: 406 average time/residue: 0.5550 time to fit residues: 355.4064 Evaluate side-chains 337 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 319 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2592 ASN Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 4167 VAL Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 5112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 334 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 402 optimal weight: 4.9990 chunk 434 optimal weight: 0.9990 chunk 358 optimal weight: 0.9990 chunk 398 optimal weight: 1.9990 chunk 137 optimal weight: 0.0070 chunk 322 optimal weight: 3.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 HIS ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 GLN A1057 GLN ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 HIS ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1882 HIS A2136 HIS A3542 GLN ** A3561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5014 GLN A5146 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35961 Z= 0.223 Angle : 0.605 11.759 48670 Z= 0.302 Chirality : 0.041 0.210 5512 Planarity : 0.004 0.107 6228 Dihedral : 5.869 84.358 4797 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.62 % Favored : 92.31 % Rotamer: Outliers : 1.51 % Allowed : 8.05 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 4320 helix: 0.31 (0.10), residues: 2480 sheet: -0.30 (0.34), residues: 227 loop : -2.36 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1298 HIS 0.011 0.001 HIS A 803 PHE 0.038 0.002 PHE A2371 TYR 0.022 0.001 TYR A1717 ARG 0.005 0.000 ARG A3493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 350 time to evaluate : 4.395 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: A 663 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7451 (mtp180) REVERT: A 934 MET cc_start: 0.7450 (ttp) cc_final: 0.7240 (ttm) REVERT: A 940 GLN cc_start: 0.7456 (mt0) cc_final: 0.6735 (tm-30) REVERT: A 1120 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7506 (mmt180) REVERT: A 1243 ASN cc_start: 0.7923 (m110) cc_final: 0.7493 (m110) REVERT: A 1373 ILE cc_start: 0.5796 (OUTLIER) cc_final: 0.5516 (mt) REVERT: A 1405 LYS cc_start: 0.8478 (mptt) cc_final: 0.8267 (mmtp) REVERT: A 1409 ASP cc_start: 0.7975 (m-30) cc_final: 0.7711 (m-30) REVERT: A 1596 MET cc_start: 0.8152 (mmm) cc_final: 0.7908 (mmm) REVERT: A 1864 TYR cc_start: 0.7897 (t80) cc_final: 0.7662 (t80) REVERT: A 1936 LEU cc_start: 0.7503 (tt) cc_final: 0.7283 (tp) REVERT: A 2258 ARG cc_start: 0.6813 (pmt170) cc_final: 0.6219 (ptt-90) REVERT: A 2495 MET cc_start: 0.8092 (tpp) cc_final: 0.7445 (tpt) REVERT: A 2648 MET cc_start: 0.8644 (mmm) cc_final: 0.8174 (mmp) REVERT: A 2753 PHE cc_start: 0.7641 (m-80) cc_final: 0.7336 (m-80) REVERT: A 2977 GLU cc_start: 0.7563 (pt0) cc_final: 0.7311 (pt0) REVERT: A 3382 MET cc_start: 0.8805 (mmm) cc_final: 0.8438 (mmm) REVERT: A 3503 MET cc_start: 0.7400 (mmm) cc_final: 0.7198 (mmm) REVERT: A 3552 ARG cc_start: 0.7601 (tpp-160) cc_final: 0.7278 (mmp-170) REVERT: A 3619 LYS cc_start: 0.8665 (pmmt) cc_final: 0.8449 (ptpp) REVERT: A 3636 MET cc_start: 0.3493 (tpp) cc_final: 0.2350 (ptt) outliers start: 59 outliers final: 29 residues processed: 400 average time/residue: 0.5620 time to fit residues: 355.0586 Evaluate side-chains 348 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 318 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2881 SER Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3536 ASN Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4167 VAL Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5112 SER Chi-restraints excluded: chain A residue 5117 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 0.0870 chunk 302 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 403 optimal weight: 0.9990 chunk 427 optimal weight: 4.9990 chunk 210 optimal weight: 0.4980 chunk 382 optimal weight: 0.0770 chunk 115 optimal weight: 0.0020 overall best weight: 0.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 ASN A 796 HIS ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2942 HIS ** A3561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3864 GLN A3964 HIS A4134 GLN ** A4196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4883 GLN ** A5121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5146 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35961 Z= 0.132 Angle : 0.548 9.461 48670 Z= 0.273 Chirality : 0.039 0.179 5512 Planarity : 0.004 0.066 6228 Dihedral : 5.409 88.920 4796 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.36 % Allowed : 9.10 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.46 (0.13), residues: 4320 helix: 0.86 (0.11), residues: 2483 sheet: -0.10 (0.35), residues: 224 loop : -2.24 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1298 HIS 0.006 0.001 HIS A 796 PHE 0.030 0.001 PHE A2371 TYR 0.023 0.001 TYR A1717 ARG 0.005 0.000 ARG A1386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 356 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 ASP cc_start: 0.6595 (m-30) cc_final: 0.6156 (m-30) REVERT: A 646 ARG cc_start: 0.6692 (tpp80) cc_final: 0.6465 (ttp80) REVERT: A 677 LYS cc_start: 0.6835 (mmtp) cc_final: 0.6509 (mtmm) REVERT: A 934 MET cc_start: 0.7406 (ttp) cc_final: 0.7130 (ttm) REVERT: A 940 GLN cc_start: 0.7407 (mt0) cc_final: 0.6819 (tm-30) REVERT: A 1247 ASP cc_start: 0.8172 (m-30) cc_final: 0.7932 (m-30) REVERT: A 1307 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7959 (ttmm) REVERT: A 1382 GLU cc_start: 0.7134 (tt0) cc_final: 0.6715 (tt0) REVERT: A 1409 ASP cc_start: 0.7946 (m-30) cc_final: 0.7741 (m-30) REVERT: A 1596 MET cc_start: 0.8005 (mmm) cc_final: 0.7776 (mmm) REVERT: A 1864 TYR cc_start: 0.7733 (t80) cc_final: 0.7506 (t80) REVERT: A 2258 ARG cc_start: 0.6704 (pmt170) cc_final: 0.6262 (mtm110) REVERT: A 2324 ILE cc_start: 0.7545 (mt) cc_final: 0.7195 (mt) REVERT: A 2495 MET cc_start: 0.8168 (tpp) cc_final: 0.7749 (tpt) REVERT: A 2554 TYR cc_start: 0.7596 (m-80) cc_final: 0.7247 (m-80) REVERT: A 2648 MET cc_start: 0.8551 (mmm) cc_final: 0.8054 (mmt) REVERT: A 2753 PHE cc_start: 0.7732 (m-80) cc_final: 0.7506 (m-80) REVERT: A 3331 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7878 (mtm-85) REVERT: A 3511 ASP cc_start: 0.8169 (m-30) cc_final: 0.7838 (m-30) REVERT: A 3552 ARG cc_start: 0.7466 (tpp-160) cc_final: 0.7214 (mmp-170) REVERT: A 3619 LYS cc_start: 0.8639 (pmmt) cc_final: 0.8434 (ptpp) REVERT: A 3636 MET cc_start: 0.2716 (tpp) cc_final: 0.1960 (ptt) REVERT: A 3981 MET cc_start: 0.7916 (ttp) cc_final: 0.7709 (ptm) REVERT: A 4348 LYS cc_start: 0.7938 (tptp) cc_final: 0.7734 (tptp) REVERT: A 4782 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8493 (mt) REVERT: A 5005 GLN cc_start: 0.7082 (mt0) cc_final: 0.6815 (mm-40) REVERT: A 5146 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8090 (pp30) outliers start: 53 outliers final: 32 residues processed: 397 average time/residue: 0.5580 time to fit residues: 355.3797 Evaluate side-chains 355 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 320 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2773 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3331 ARG Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4392 MET Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5112 SER Chi-restraints excluded: chain A residue 5146 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 318 optimal weight: 0.0980 chunk 176 optimal weight: 0.6980 chunk 364 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 218 optimal weight: 3.9990 chunk 383 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1092 GLN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1741 GLN A2126 GLN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4634 HIS ** A5121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35961 Z= 0.169 Angle : 0.550 9.044 48670 Z= 0.275 Chirality : 0.040 0.188 5512 Planarity : 0.004 0.066 6228 Dihedral : 5.303 88.160 4796 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.27 % Favored : 92.71 % Rotamer: Outliers : 1.82 % Allowed : 9.51 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.19 (0.13), residues: 4320 helix: 1.07 (0.11), residues: 2489 sheet: 0.02 (0.35), residues: 224 loop : -2.13 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1298 HIS 0.028 0.001 HIS A3964 PHE 0.032 0.001 PHE A2371 TYR 0.022 0.001 TYR A1717 ARG 0.005 0.000 ARG A5042 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 340 time to evaluate : 4.030 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: A 934 MET cc_start: 0.7311 (ttp) cc_final: 0.7109 (ttm) REVERT: A 940 GLN cc_start: 0.7401 (mt0) cc_final: 0.6822 (tm-30) REVERT: A 1247 ASP cc_start: 0.8180 (m-30) cc_final: 0.7945 (m-30) REVERT: A 1307 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7955 (ttmm) REVERT: A 1409 ASP cc_start: 0.7808 (m-30) cc_final: 0.7589 (m-30) REVERT: A 1633 GLN cc_start: 0.7741 (mp10) cc_final: 0.7473 (mp10) REVERT: A 1864 TYR cc_start: 0.7747 (t80) cc_final: 0.7509 (t80) REVERT: A 2258 ARG cc_start: 0.6708 (pmt170) cc_final: 0.6299 (mtm110) REVERT: A 2324 ILE cc_start: 0.7475 (mt) cc_final: 0.7166 (mt) REVERT: A 2495 MET cc_start: 0.8230 (tpp) cc_final: 0.7783 (tpt) REVERT: A 2543 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: A 2554 TYR cc_start: 0.7584 (m-80) cc_final: 0.7217 (m-80) REVERT: A 2648 MET cc_start: 0.8528 (mmm) cc_final: 0.8107 (mmt) REVERT: A 3331 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7854 (mtm-85) REVERT: A 3552 ARG cc_start: 0.7509 (tpp-160) cc_final: 0.7245 (mmp-170) REVERT: A 3636 MET cc_start: 0.2696 (tpp) cc_final: 0.1807 (ptt) REVERT: A 4348 LYS cc_start: 0.8023 (tptp) cc_final: 0.7822 (tptp) REVERT: A 4782 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8566 (mt) REVERT: A 5005 GLN cc_start: 0.7229 (mt0) cc_final: 0.7028 (mm-40) outliers start: 71 outliers final: 45 residues processed: 396 average time/residue: 0.5507 time to fit residues: 352.3993 Evaluate side-chains 359 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 312 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3517 ASN Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3944 ILE Chi-restraints excluded: chain A residue 3964 HIS Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4392 MET Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 2.9990 chunk 384 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 427 optimal weight: 0.8980 chunk 355 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 224 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS A 803 HIS ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3785 HIS ** A4196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4634 HIS A4900 GLN ** A5121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35961 Z= 0.217 Angle : 0.578 11.402 48670 Z= 0.287 Chirality : 0.041 0.197 5512 Planarity : 0.004 0.063 6228 Dihedral : 5.309 78.107 4796 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.82 % Allowed : 10.10 % Favored : 88.08 % 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: -0.03 (0.13), residues: 4320 helix: 1.21 (0.11), residues: 2480 sheet: 0.21 (0.36), residues: 215 loop : -2.07 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1601 HIS 0.025 0.001 HIS A3964 PHE 0.033 0.002 PHE A2371 TYR 0.023 0.001 TYR A1717 ARG 0.004 0.000 ARG A3525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 331 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 LYS cc_start: 0.6848 (mmtp) cc_final: 0.6487 (mtmm) REVERT: A 785 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7951 (pttm) REVERT: A 934 MET cc_start: 0.7447 (ttp) cc_final: 0.7222 (ttm) REVERT: A 940 GLN cc_start: 0.7361 (mt0) cc_final: 0.6806 (tm-30) REVERT: A 1247 ASP cc_start: 0.8192 (m-30) cc_final: 0.7960 (m-30) REVERT: A 1307 LYS cc_start: 0.8325 (ttmm) cc_final: 0.8026 (ttmm) REVERT: A 1409 ASP cc_start: 0.7821 (m-30) cc_final: 0.7610 (m-30) REVERT: A 1519 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8206 (mmtm) REVERT: A 1864 TYR cc_start: 0.7819 (t80) cc_final: 0.7602 (t80) REVERT: A 2258 ARG cc_start: 0.6717 (pmt170) cc_final: 0.6289 (mtm110) REVERT: A 2324 ILE cc_start: 0.7521 (mt) cc_final: 0.7295 (mt) REVERT: A 2495 MET cc_start: 0.8216 (tpp) cc_final: 0.7492 (tpt) REVERT: A 2543 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: A 2554 TYR cc_start: 0.7462 (m-80) cc_final: 0.7105 (m-80) REVERT: A 2648 MET cc_start: 0.8543 (mmm) cc_final: 0.8185 (mmt) REVERT: A 3331 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7828 (mtm-85) REVERT: A 3552 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7412 (mmp-170) REVERT: A 3636 MET cc_start: 0.2521 (tpp) cc_final: 0.1770 (ptt) REVERT: A 4348 LYS cc_start: 0.8068 (tptp) cc_final: 0.7838 (tptp) REVERT: A 4519 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5541 (pmm150) REVERT: A 4537 MET cc_start: 0.8245 (mtp) cc_final: 0.8036 (mtp) outliers start: 71 outliers final: 46 residues processed: 383 average time/residue: 0.5243 time to fit residues: 320.5450 Evaluate side-chains 364 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 316 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2592 ASN Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3517 ASN Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4074 VAL Chi-restraints excluded: chain A residue 4519 ARG Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 312 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 chunk 359 optimal weight: 0.0050 chunk 238 optimal weight: 1.9990 chunk 426 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 196 optimal weight: 0.0370 overall best weight: 1.1476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 HIS A1255 ASN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1595 ASN A1812 GLN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4957 GLN A4990 ASN A5146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35961 Z= 0.236 Angle : 0.583 10.814 48670 Z= 0.288 Chirality : 0.041 0.200 5512 Planarity : 0.004 0.068 6228 Dihedral : 5.310 78.490 4796 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.62 % Favored : 92.36 % Rotamer: Outliers : 1.82 % Allowed : 10.18 % Favored : 88.00 % 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: 0.03 (0.13), residues: 4320 helix: 1.27 (0.11), residues: 2481 sheet: 0.20 (0.36), residues: 215 loop : -2.06 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1298 HIS 0.018 0.001 HIS A3964 PHE 0.042 0.002 PHE A3638 TYR 0.023 0.001 TYR A1717 ARG 0.006 0.000 ARG A3345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 324 time to evaluate : 4.114 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 934 MET cc_start: 0.7458 (ttp) cc_final: 0.7237 (ttm) REVERT: A 940 GLN cc_start: 0.7390 (mt0) cc_final: 0.6811 (tm-30) REVERT: A 1247 ASP cc_start: 0.8204 (m-30) cc_final: 0.7970 (m-30) REVERT: A 1307 LYS cc_start: 0.8333 (ttmm) cc_final: 0.8026 (ttmm) REVERT: A 1394 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8322 (mp) REVERT: A 1409 ASP cc_start: 0.7825 (m-30) cc_final: 0.7614 (m-30) REVERT: A 1519 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8207 (mmtm) REVERT: A 1864 TYR cc_start: 0.7814 (t80) cc_final: 0.7569 (t80) REVERT: A 2258 ARG cc_start: 0.6729 (pmt170) cc_final: 0.6261 (mtm110) REVERT: A 2324 ILE cc_start: 0.7526 (mt) cc_final: 0.7309 (mt) REVERT: A 2495 MET cc_start: 0.8235 (tpp) cc_final: 0.7392 (tpt) REVERT: A 2543 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: A 2648 MET cc_start: 0.8540 (mmm) cc_final: 0.8197 (mmp) REVERT: A 2691 ASP cc_start: 0.8322 (m-30) cc_final: 0.8018 (m-30) REVERT: A 3331 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7870 (mtm-85) REVERT: A 3552 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7409 (mmp-170) REVERT: A 3636 MET cc_start: 0.2463 (tpp) cc_final: 0.1591 (ptt) REVERT: A 3638 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.5899 (t80) REVERT: A 3981 MET cc_start: 0.7493 (tmm) cc_final: 0.7215 (tmm) REVERT: A 4348 LYS cc_start: 0.8092 (tptp) cc_final: 0.7850 (tptp) REVERT: A 4519 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.5642 (pmm150) outliers start: 71 outliers final: 54 residues processed: 371 average time/residue: 0.5391 time to fit residues: 318.2408 Evaluate side-chains 379 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 321 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2216 MET Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2592 ASN Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3512 LEU Chi-restraints excluded: chain A residue 3517 ASN Chi-restraints excluded: chain A residue 3638 PHE Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4074 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4513 VAL Chi-restraints excluded: chain A residue 4519 ARG Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5112 SER Chi-restraints excluded: chain A residue 5117 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 270 optimal weight: 0.7980 chunk 290 optimal weight: 0.0060 chunk 210 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN A 803 HIS A1595 ASN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4634 HIS ** A5047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35961 Z= 0.168 Angle : 0.558 10.704 48670 Z= 0.276 Chirality : 0.040 0.184 5512 Planarity : 0.004 0.067 6228 Dihedral : 5.203 85.379 4796 Min Nonbonded Distance : 1.604 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.74 % Allowed : 10.48 % Favored : 87.77 % 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: 0.20 (0.13), residues: 4320 helix: 1.42 (0.11), residues: 2484 sheet: 0.25 (0.36), residues: 215 loop : -2.02 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1601 HIS 0.030 0.001 HIS A3964 PHE 0.030 0.001 PHE A2371 TYR 0.026 0.001 TYR A1750 ARG 0.006 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 326 time to evaluate : 3.929 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: A 646 ARG cc_start: 0.6889 (ttp80) cc_final: 0.6667 (ttt90) REVERT: A 934 MET cc_start: 0.7452 (ttp) cc_final: 0.7235 (ttm) REVERT: A 940 GLN cc_start: 0.7328 (mt0) cc_final: 0.6782 (tm-30) REVERT: A 1247 ASP cc_start: 0.8180 (m-30) cc_final: 0.7954 (m-30) REVERT: A 1307 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7993 (ttmm) REVERT: A 1409 ASP cc_start: 0.7805 (m-30) cc_final: 0.7575 (m-30) REVERT: A 1519 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8232 (mmtm) REVERT: A 1864 TYR cc_start: 0.7781 (t80) cc_final: 0.7545 (t80) REVERT: A 2258 ARG cc_start: 0.6700 (pmt170) cc_final: 0.6236 (mtm110) REVERT: A 2324 ILE cc_start: 0.7596 (mt) cc_final: 0.7330 (mt) REVERT: A 2495 MET cc_start: 0.8232 (tpp) cc_final: 0.7399 (tpt) REVERT: A 2543 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: A 2648 MET cc_start: 0.8457 (mmm) cc_final: 0.8126 (mmt) REVERT: A 2658 LEU cc_start: 0.8474 (mt) cc_final: 0.8271 (mt) REVERT: A 2691 ASP cc_start: 0.8297 (m-30) cc_final: 0.8018 (m-30) REVERT: A 2923 MET cc_start: 0.8740 (mtp) cc_final: 0.8538 (mtp) REVERT: A 3331 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7869 (mtm-85) REVERT: A 3552 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7410 (mmp-170) REVERT: A 3636 MET cc_start: 0.2176 (tpp) cc_final: 0.1112 (ptt) REVERT: A 3638 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.6124 (t80) REVERT: A 3981 MET cc_start: 0.7531 (tmm) cc_final: 0.7200 (tmm) REVERT: A 4348 LYS cc_start: 0.8048 (tptp) cc_final: 0.7806 (tptp) REVERT: A 4421 MET cc_start: 0.8573 (mmm) cc_final: 0.8341 (mmm) REVERT: A 4782 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8582 (mt) outliers start: 68 outliers final: 54 residues processed: 374 average time/residue: 0.5362 time to fit residues: 320.1902 Evaluate side-chains 374 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 317 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1595 ASN Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2592 ASN Chi-restraints excluded: chain A residue 2628 HIS Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2773 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3517 ASN Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3638 PHE Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3944 ILE Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4238 MET Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4392 MET Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5112 SER Chi-restraints excluded: chain A residue 5117 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 5.9990 chunk 408 optimal weight: 0.9990 chunk 372 optimal weight: 3.9990 chunk 396 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 311 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 358 optimal weight: 0.0270 chunk 375 optimal weight: 0.0870 chunk 395 optimal weight: 1.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS A 803 HIS A1595 ASN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4001 HIS ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5047 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35961 Z= 0.155 Angle : 0.550 10.521 48670 Z= 0.272 Chirality : 0.040 0.178 5512 Planarity : 0.004 0.067 6228 Dihedral : 5.126 89.023 4796 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.54 % Allowed : 10.72 % Favored : 87.75 % 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: 0.30 (0.13), residues: 4320 helix: 1.51 (0.11), residues: 2476 sheet: 0.28 (0.36), residues: 215 loop : -1.96 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1298 HIS 0.026 0.001 HIS A3964 PHE 0.028 0.001 PHE A2371 TYR 0.029 0.001 TYR A1750 ARG 0.006 0.000 ARG A5016 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 324 time to evaluate : 4.314 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 934 MET cc_start: 0.7444 (ttp) cc_final: 0.7230 (ttm) REVERT: A 940 GLN cc_start: 0.7285 (mt0) cc_final: 0.6756 (tm-30) REVERT: A 1134 VAL cc_start: 0.8435 (t) cc_final: 0.8198 (p) REVERT: A 1307 LYS cc_start: 0.8288 (ttmm) cc_final: 0.8088 (ttmt) REVERT: A 1394 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 1409 ASP cc_start: 0.7797 (m-30) cc_final: 0.7567 (m-30) REVERT: A 1519 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8242 (mmtm) REVERT: A 1864 TYR cc_start: 0.7782 (t80) cc_final: 0.7543 (t80) REVERT: A 2012 MET cc_start: 0.4888 (mpm) cc_final: 0.4348 (mmp) REVERT: A 2258 ARG cc_start: 0.6683 (pmt170) cc_final: 0.6218 (mtm110) REVERT: A 2324 ILE cc_start: 0.7602 (mt) cc_final: 0.7238 (mt) REVERT: A 2495 MET cc_start: 0.8242 (tpp) cc_final: 0.7428 (tpt) REVERT: A 2543 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: A 2648 MET cc_start: 0.8420 (mmm) cc_final: 0.8097 (mmt) REVERT: A 2691 ASP cc_start: 0.8293 (m-30) cc_final: 0.8013 (m-30) REVERT: A 2923 MET cc_start: 0.8736 (mtp) cc_final: 0.8525 (mtp) REVERT: A 3331 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7884 (mtm-85) REVERT: A 3552 ARG cc_start: 0.7689 (tpp-160) cc_final: 0.7397 (mmp-170) REVERT: A 3636 MET cc_start: 0.2191 (tpp) cc_final: 0.1246 (ptt) REVERT: A 3638 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.6177 (t80) REVERT: A 3981 MET cc_start: 0.7510 (tmm) cc_final: 0.7164 (tmm) REVERT: A 4421 MET cc_start: 0.8579 (mmm) cc_final: 0.8345 (mmm) REVERT: A 4782 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8570 (mt) outliers start: 60 outliers final: 51 residues processed: 368 average time/residue: 0.5270 time to fit residues: 311.5450 Evaluate side-chains 369 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 314 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1595 ASN Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2592 ASN Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2773 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3512 LEU Chi-restraints excluded: chain A residue 3517 ASN Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3638 PHE Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3944 ILE Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4238 MET Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4392 MET Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5112 SER Chi-restraints excluded: chain A residue 5117 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 0.8980 chunk 419 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 291 optimal weight: 0.0980 chunk 440 optimal weight: 5.9990 chunk 405 optimal weight: 2.9990 chunk 350 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 HIS A1595 ASN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4634 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35961 Z= 0.200 Angle : 0.570 10.664 48670 Z= 0.282 Chirality : 0.040 0.187 5512 Planarity : 0.004 0.068 6228 Dihedral : 5.167 86.998 4796 Min Nonbonded Distance : 1.566 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.59 % Allowed : 10.82 % Favored : 87.59 % 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 (0.13), residues: 4320 helix: 1.49 (0.11), residues: 2483 sheet: 0.29 (0.36), residues: 215 loop : -1.99 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1298 HIS 0.023 0.001 HIS A3964 PHE 0.037 0.001 PHE A2371 TYR 0.030 0.001 TYR A1750 ARG 0.008 0.000 ARG A3525 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 317 time to evaluate : 4.292 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 934 MET cc_start: 0.7442 (ttp) cc_final: 0.7209 (ttm) REVERT: A 940 GLN cc_start: 0.7339 (mt0) cc_final: 0.6796 (tm-30) REVERT: A 1238 LEU cc_start: 0.7793 (tp) cc_final: 0.7526 (tp) REVERT: A 1307 LYS cc_start: 0.8326 (ttmm) cc_final: 0.8126 (ttmt) REVERT: A 1394 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 1409 ASP cc_start: 0.7822 (m-30) cc_final: 0.7591 (m-30) REVERT: A 1519 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8250 (mmtm) REVERT: A 1864 TYR cc_start: 0.7792 (t80) cc_final: 0.7554 (t80) REVERT: A 2012 MET cc_start: 0.4723 (mpm) cc_final: 0.4193 (mmp) REVERT: A 2258 ARG cc_start: 0.6698 (pmt170) cc_final: 0.6232 (mtm110) REVERT: A 2324 ILE cc_start: 0.7617 (mt) cc_final: 0.7346 (mt) REVERT: A 2495 MET cc_start: 0.8243 (tpp) cc_final: 0.7408 (tpt) REVERT: A 2543 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: A 2648 MET cc_start: 0.8431 (mmm) cc_final: 0.8108 (mmt) REVERT: A 2691 ASP cc_start: 0.8305 (m-30) cc_final: 0.8017 (m-30) REVERT: A 3331 ARG cc_start: 0.8139 (mtt90) cc_final: 0.7892 (mtm-85) REVERT: A 3552 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7405 (mmp-170) REVERT: A 3636 MET cc_start: 0.2340 (tpp) cc_final: 0.1250 (ptt) REVERT: A 3858 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.6067 (ttm) REVERT: A 3981 MET cc_start: 0.7469 (tmm) cc_final: 0.7106 (tmm) REVERT: A 4421 MET cc_start: 0.8570 (mmm) cc_final: 0.8335 (mmm) REVERT: A 4782 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8631 (mt) outliers start: 62 outliers final: 54 residues processed: 365 average time/residue: 0.5377 time to fit residues: 315.1726 Evaluate side-chains 372 residues out of total 3911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 314 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 803 HIS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1427 CYS Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1595 ASN Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 2151 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain A residue 2295 ASN Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2574 CYS Chi-restraints excluded: chain A residue 2592 ASN Chi-restraints excluded: chain A residue 2707 LEU Chi-restraints excluded: chain A residue 2773 HIS Chi-restraints excluded: chain A residue 2807 VAL Chi-restraints excluded: chain A residue 2924 VAL Chi-restraints excluded: chain A residue 2964 LEU Chi-restraints excluded: chain A residue 3023 GLN Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3245 GLU Chi-restraints excluded: chain A residue 3367 THR Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3512 LEU Chi-restraints excluded: chain A residue 3517 ASN Chi-restraints excluded: chain A residue 3524 LEU Chi-restraints excluded: chain A residue 3641 VAL Chi-restraints excluded: chain A residue 3647 LEU Chi-restraints excluded: chain A residue 3722 MET Chi-restraints excluded: chain A residue 3858 MET Chi-restraints excluded: chain A residue 3919 ARG Chi-restraints excluded: chain A residue 3944 ILE Chi-restraints excluded: chain A residue 3968 LEU Chi-restraints excluded: chain A residue 3997 VAL Chi-restraints excluded: chain A residue 4038 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4238 MET Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4392 MET Chi-restraints excluded: chain A residue 4635 LEU Chi-restraints excluded: chain A residue 4671 HIS Chi-restraints excluded: chain A residue 4782 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4941 MET Chi-restraints excluded: chain A residue 5040 LEU Chi-restraints excluded: chain A residue 5112 SER Chi-restraints excluded: chain A residue 5117 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 0.3980 chunk 373 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 323 optimal weight: 0.0050 chunk 51 optimal weight: 0.0370 chunk 97 optimal weight: 0.7980 chunk 351 optimal weight: 0.9980 chunk 146 optimal weight: 0.1980 chunk 360 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.2872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 HIS A1595 ASN ** A3608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4634 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.101774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081140 restraints weight = 73711.938| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.06 r_work: 0.3080 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35961 Z= 0.135 Angle : 0.544 10.465 48670 Z= 0.270 Chirality : 0.039 0.175 5512 Planarity : 0.004 0.067 6228 Dihedral : 5.004 87.495 4796 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.44 % Allowed : 10.95 % Favored : 87.62 % 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: 0.42 (0.13), residues: 4320 helix: 1.61 (0.11), residues: 2480 sheet: 0.35 (0.36), residues: 214 loop : -1.94 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1298 HIS 0.021 0.001 HIS A3964 PHE 0.029 0.001 PHE A2371 TYR 0.023 0.001 TYR A1717 ARG 0.008 0.000 ARG A3525 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8177.65 seconds wall clock time: 150 minutes 46.19 seconds (9046.19 seconds total)