Starting phenix.real_space_refine on Mon Jun 23 05:58:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e0q_27822/06_2025/8e0q_27822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e0q_27822/06_2025/8e0q_27822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e0q_27822/06_2025/8e0q_27822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e0q_27822/06_2025/8e0q_27822.map" model { file = "/net/cci-nas-00/data/ceres_data/8e0q_27822/06_2025/8e0q_27822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e0q_27822/06_2025/8e0q_27822.cif" } resolution = 2.66 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 200 5.16 5 C 16796 2.51 5 N 4654 2.21 5 O 4948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26604 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1689, 13299 Classifications: {'peptide': 1689} Link IDs: {'PTRANS': 98, 'TRANS': 1590} Chain breaks: 12 Chain: "B" Number of atoms: 13299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1689, 13299 Classifications: {'peptide': 1689} Link IDs: {'PTRANS': 98, 'TRANS': 1590} Chain breaks: 12 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4839 SG CYS A1179 29.914 81.981 48.553 1.00 64.43 S ATOM 5064 SG CYS A1208 33.259 83.628 49.452 1.00 63.36 S ATOM 5086 SG CYS A1211 32.975 79.900 49.407 1.00 77.01 S ATOM 5249 SG CYS A1232 32.699 81.849 46.102 1.00 84.41 S ATOM 5086 SG CYS A1211 32.975 79.900 49.407 1.00 77.01 S ATOM 5115 SG CYS A1215 33.121 76.514 51.096 1.00 69.75 S ATOM 5263 SG CYS A1234 33.277 76.815 47.200 1.00100.10 S ATOM 5316 SG CYS A1240 30.103 77.397 49.148 1.00 54.66 S ATOM 4979 SG CYS A1196 41.505 74.723 46.339 1.00 69.26 S ATOM 5003 SG CYS A1199 38.417 72.246 46.297 1.00 59.43 S ATOM 18138 SG CYS B1179 117.399 149.787 48.574 1.00 60.28 S ATOM 18363 SG CYS B1208 114.003 148.226 49.509 1.00 53.97 S ATOM 18385 SG CYS B1211 114.393 151.922 49.406 1.00 65.22 S ATOM 18548 SG CYS B1232 114.597 149.905 46.129 1.00 78.85 S ATOM 18385 SG CYS B1211 114.393 151.922 49.406 1.00 65.22 S ATOM 18414 SG CYS B1215 114.314 155.324 51.124 1.00 70.02 S ATOM 18562 SG CYS B1234 114.086 154.999 47.262 1.00 94.82 S ATOM 18615 SG CYS B1240 117.324 154.367 49.177 1.00 63.91 S ATOM 18278 SG CYS B1196 105.769 156.952 46.368 1.00 65.55 S ATOM 18302 SG CYS B1199 109.017 159.156 46.164 1.00 60.54 S Time building chain proxies: 18.91, per 1000 atoms: 0.71 Number of scatterers: 26604 At special positions: 0 Unit cell: (149.04, 232.668, 103.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 200 16.00 O 4948 8.00 N 4654 7.00 C 16796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.33 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2801 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1232 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1179 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1208 " pdb="ZN ZN A2801 " - pdb=" SG CYS A1211 " pdb=" ZN A2802 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1240 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1215 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1211 " pdb="ZN ZN A2802 " - pdb=" SG CYS A1234 " pdb=" ZN A2803 " pdb="ZN ZN A2803 " - pdb=" ND1 HIS A1216 " pdb="ZN ZN A2803 " - pdb=" ND1 HIS A1219 " pdb="ZN ZN A2803 " - pdb=" SG CYS A1199 " pdb="ZN ZN A2803 " - pdb=" SG CYS A1196 " pdb=" ZN B2801 " pdb="ZN ZN B2801 " - pdb=" SG CYS B1232 " pdb="ZN ZN B2801 " - pdb=" SG CYS B1179 " pdb="ZN ZN B2801 " - pdb=" SG CYS B1208 " pdb="ZN ZN B2801 " - pdb=" SG CYS B1211 " pdb=" ZN B2802 " pdb="ZN ZN B2802 " - pdb=" SG CYS B1240 " pdb="ZN ZN B2802 " - pdb=" SG CYS B1215 " pdb="ZN ZN B2802 " - pdb=" SG CYS B1211 " pdb="ZN ZN B2802 " - pdb=" SG CYS B1234 " pdb=" ZN B2803 " pdb="ZN ZN B2803 " - pdb=" ND1 HIS B1216 " pdb="ZN ZN B2803 " - pdb=" ND1 HIS B1219 " pdb="ZN ZN B2803 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2803 " - pdb=" SG CYS B1196 " Number of angles added : 28 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6436 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 27 sheets defined 49.1% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 14 through 31 removed outlier: 3.759A pdb=" N LEU A 18 " --> pdb=" O THR A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.826A pdb=" N GLN A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.763A pdb=" N LEU A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 459' Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.536A pdb=" N ASN A 513 " --> pdb=" O ARG A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.758A pdb=" N LEU A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS A 583 " --> pdb=" O PRO A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 583' Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 799 removed outlier: 4.077A pdb=" N ASN A 798 " --> pdb=" O ASN A 795 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 795 through 799' Processing helix chain 'A' and resid 874 through 882 Processing helix chain 'A' and resid 884 through 902 Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'A' and resid 1077 through 1095 Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 4.477A pdb=" N ARG A1103 " --> pdb=" O GLN A1099 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU A1104 " --> pdb=" O PRO A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1125 through 1142 Processing helix chain 'A' and resid 1149 through 1159 removed outlier: 3.713A pdb=" N GLY A1156 " --> pdb=" O ASP A1152 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET A1157 " --> pdb=" O VAL A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1167 Processing helix chain 'A' and resid 1168 through 1176 Processing helix chain 'A' and resid 1180 through 1185 Processing helix chain 'A' and resid 1233 through 1237 removed outlier: 3.508A pdb=" N LYS A1237 " --> pdb=" O CYS A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1262 removed outlier: 3.552A pdb=" N THR A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1267 Processing helix chain 'A' and resid 1274 through 1291 removed outlier: 3.546A pdb=" N VAL A1288 " --> pdb=" O ALA A1284 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS A1291 " --> pdb=" O THR A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1334 removed outlier: 4.090A pdb=" N LEU A1327 " --> pdb=" O ARG A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1344 Processing helix chain 'A' and resid 1364 through 1374 removed outlier: 3.888A pdb=" N GLN A1374 " --> pdb=" O TYR A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1389 Processing helix chain 'A' and resid 1395 through 1410 Processing helix chain 'A' and resid 1416 through 1443 Processing helix chain 'A' and resid 1447 through 1451 removed outlier: 4.096A pdb=" N ASN A1451 " --> pdb=" O LYS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1467 Processing helix chain 'A' and resid 1467 through 1489 removed outlier: 3.951A pdb=" N GLU A1473 " --> pdb=" O PRO A1469 " (cutoff:3.500A) Proline residue: A1485 - end of helix Processing helix chain 'A' and resid 1502 through 1515 removed outlier: 3.820A pdb=" N GLN A1508 " --> pdb=" O ILE A1504 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY A1509 " --> pdb=" O ASP A1505 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A1510 " --> pdb=" O ALA A1506 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU A1512 " --> pdb=" O GLN A1508 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1718 removed outlier: 3.691A pdb=" N GLN A1715 " --> pdb=" O ARG A1712 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP A1716 " --> pdb=" O SER A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1802 removed outlier: 3.662A pdb=" N SER A1780 " --> pdb=" O SER A1776 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1809 Processing helix chain 'A' and resid 1820 through 1863 Proline residue: A1837 - end of helix Processing helix chain 'A' and resid 1873 through 1877 Processing helix chain 'A' and resid 1912 through 1928 removed outlier: 3.557A pdb=" N HIS A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1940 through 1943 Processing helix chain 'A' and resid 1944 through 1966 Processing helix chain 'A' and resid 2020 through 2024 Processing helix chain 'A' and resid 2043 through 2048 Processing helix chain 'A' and resid 2048 through 2053 removed outlier: 3.841A pdb=" N ASP A2052 " --> pdb=" O ILE A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2057 removed outlier: 4.165A pdb=" N LEU A2057 " --> pdb=" O PRO A2054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2054 through 2057' Processing helix chain 'A' and resid 2062 through 2067 removed outlier: 3.571A pdb=" N LEU A2066 " --> pdb=" O ARG A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2102 Proline residue: A2099 - end of helix removed outlier: 4.557A pdb=" N MET A2102 " --> pdb=" O LEU A2098 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2169 removed outlier: 3.964A pdb=" N PHE A2169 " --> pdb=" O LEU A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2181 through 2189 Processing helix chain 'A' and resid 2189 through 2200 removed outlier: 3.503A pdb=" N ARG A2198 " --> pdb=" O GLU A2194 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2207 Processing helix chain 'A' and resid 2210 through 2215 Processing helix chain 'A' and resid 2217 through 2234 removed outlier: 3.606A pdb=" N LYS A2221 " --> pdb=" O GLY A2217 " (cutoff:3.500A) Processing helix chain 'A' and resid 2248 through 2263 Processing helix chain 'A' and resid 2288 through 2304 removed outlier: 3.612A pdb=" N ALA A2292 " --> pdb=" O GLY A2288 " (cutoff:3.500A) Processing helix chain 'A' and resid 2522 through 2542 Processing helix chain 'A' and resid 2551 through 2560 Processing helix chain 'A' and resid 2564 through 2566 No H-bonds generated for 'chain 'A' and resid 2564 through 2566' Processing helix chain 'A' and resid 2567 through 2572 Processing helix chain 'A' and resid 2572 through 2588 Processing helix chain 'A' and resid 2591 through 2599 removed outlier: 3.653A pdb=" N ASP A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2629 No H-bonds generated for 'chain 'A' and resid 2627 through 2629' Processing helix chain 'A' and resid 2630 through 2642 removed outlier: 3.972A pdb=" N TYR A2634 " --> pdb=" O ASN A2630 " (cutoff:3.500A) Processing helix chain 'A' and resid 2647 through 2660 Processing helix chain 'A' and resid 2663 through 2668 removed outlier: 3.705A pdb=" N LEU A2667 " --> pdb=" O PRO A2663 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A2668 " --> pdb=" O LYS A2664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2663 through 2668' Processing helix chain 'A' and resid 2671 through 2680 Processing helix chain 'A' and resid 2686 through 2693 removed outlier: 3.570A pdb=" N PHE A2693 " --> pdb=" O MET A2689 " (cutoff:3.500A) Processing helix chain 'A' and resid 2703 through 2720 removed outlier: 3.524A pdb=" N LEU A2707 " --> pdb=" O ASN A2703 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS A2711 " --> pdb=" O LEU A2707 " (cutoff:3.500A) Processing helix chain 'A' and resid 2722 through 2735 Processing helix chain 'A' and resid 2779 through 2793 removed outlier: 3.645A pdb=" N THR A2793 " --> pdb=" O LEU A2789 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 31 removed outlier: 3.630A pdb=" N LEU B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 46 removed outlier: 3.904A pdb=" N GLN B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 453 through 457 removed outlier: 4.284A pdb=" N SER B 456 " --> pdb=" O SER B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 511 removed outlier: 3.976A pdb=" N LEU B 506 " --> pdb=" O ARG B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 removed outlier: 3.993A pdb=" N LEU B 582 " --> pdb=" O SER B 578 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS B 583 " --> pdb=" O PRO B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 583' Processing helix chain 'B' and resid 652 through 656 removed outlier: 3.598A pdb=" N VAL B 656 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 793 Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.636A pdb=" N ASN B 857 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 858 " --> pdb=" O PRO B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 854 through 858' Processing helix chain 'B' and resid 874 through 883 Processing helix chain 'B' and resid 884 through 902 Processing helix chain 'B' and resid 904 through 913 removed outlier: 3.517A pdb=" N GLN B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 930 Processing helix chain 'B' and resid 1077 through 1094 Processing helix chain 'B' and resid 1098 through 1108 removed outlier: 4.510A pdb=" N ARG B1103 " --> pdb=" O GLN B1099 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLU B1104 " --> pdb=" O PRO B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1123 Processing helix chain 'B' and resid 1125 through 1142 Processing helix chain 'B' and resid 1149 through 1159 removed outlier: 4.131A pdb=" N MET B1157 " --> pdb=" O VAL B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1167 Processing helix chain 'B' and resid 1168 through 1176 Processing helix chain 'B' and resid 1180 through 1185 Processing helix chain 'B' and resid 1208 through 1214 Processing helix chain 'B' and resid 1247 through 1262 removed outlier: 3.661A pdb=" N THR B1262 " --> pdb=" O LEU B1258 " (cutoff:3.500A) Processing helix chain 'B' and resid 1263 through 1267 Processing helix chain 'B' and resid 1274 through 1290 removed outlier: 3.642A pdb=" N VAL B1288 " --> pdb=" O ALA B1284 " (cutoff:3.500A) Processing helix chain 'B' and resid 1291 through 1293 No H-bonds generated for 'chain 'B' and resid 1291 through 1293' Processing helix chain 'B' and resid 1323 through 1335 removed outlier: 3.929A pdb=" N LEU B1327 " --> pdb=" O ARG B1323 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B1335 " --> pdb=" O ARG B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1335 through 1344 Processing helix chain 'B' and resid 1364 through 1374 removed outlier: 3.512A pdb=" N TYR B1370 " --> pdb=" O GLU B1366 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN B1374 " --> pdb=" O TYR B1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 1377 through 1389 Processing helix chain 'B' and resid 1395 through 1410 removed outlier: 3.605A pdb=" N THR B1404 " --> pdb=" O THR B1400 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B1405 " --> pdb=" O LEU B1401 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1443 Processing helix chain 'B' and resid 1447 through 1451 removed outlier: 4.077A pdb=" N ASN B1451 " --> pdb=" O LYS B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1454 through 1467 Processing helix chain 'B' and resid 1467 through 1489 removed outlier: 3.852A pdb=" N GLU B1473 " --> pdb=" O PRO B1469 " (cutoff:3.500A) Proline residue: B1485 - end of helix Processing helix chain 'B' and resid 1502 through 1515 removed outlier: 4.350A pdb=" N GLY B1509 " --> pdb=" O ASP B1505 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B1510 " --> pdb=" O ALA B1506 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLU B1512 " --> pdb=" O GLN B1508 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1718 removed outlier: 3.610A pdb=" N GLN B1715 " --> pdb=" O ARG B1712 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP B1716 " --> pdb=" O SER B1713 " (cutoff:3.500A) Processing helix chain 'B' and resid 1776 through 1802 removed outlier: 3.717A pdb=" N SER B1780 " --> pdb=" O SER B1776 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B1802 " --> pdb=" O LEU B1798 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1809 Processing helix chain 'B' and resid 1820 through 1863 Proline residue: B1837 - end of helix Processing helix chain 'B' and resid 1873 through 1877 Processing helix chain 'B' and resid 1912 through 1928 removed outlier: 3.582A pdb=" N HIS B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) Processing helix chain 'B' and resid 1940 through 1943 Processing helix chain 'B' and resid 1944 through 1966 Processing helix chain 'B' and resid 2020 through 2024 Processing helix chain 'B' and resid 2043 through 2048 Processing helix chain 'B' and resid 2048 through 2053 removed outlier: 3.833A pdb=" N ASP B2052 " --> pdb=" O ILE B2048 " (cutoff:3.500A) Processing helix chain 'B' and resid 2054 through 2057 removed outlier: 4.202A pdb=" N LEU B2057 " --> pdb=" O PRO B2054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2054 through 2057' Processing helix chain 'B' and resid 2062 through 2068 removed outlier: 3.536A pdb=" N LEU B2066 " --> pdb=" O ARG B2062 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2103 Proline residue: B2099 - end of helix Processing helix chain 'B' and resid 2165 through 2169 removed outlier: 3.909A pdb=" N PHE B2169 " --> pdb=" O LEU B2166 " (cutoff:3.500A) Processing helix chain 'B' and resid 2181 through 2189 Processing helix chain 'B' and resid 2189 through 2200 Processing helix chain 'B' and resid 2203 through 2207 Processing helix chain 'B' and resid 2210 through 2215 Processing helix chain 'B' and resid 2217 through 2234 removed outlier: 3.757A pdb=" N LYS B2221 " --> pdb=" O GLY B2217 " (cutoff:3.500A) Processing helix chain 'B' and resid 2248 through 2263 Processing helix chain 'B' and resid 2289 through 2304 Processing helix chain 'B' and resid 2522 through 2543 Processing helix chain 'B' and resid 2551 through 2559 Processing helix chain 'B' and resid 2566 through 2572 removed outlier: 4.079A pdb=" N PHE B2570 " --> pdb=" O HIS B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2587 Processing helix chain 'B' and resid 2590 through 2599 Processing helix chain 'B' and resid 2627 through 2629 No H-bonds generated for 'chain 'B' and resid 2627 through 2629' Processing helix chain 'B' and resid 2630 through 2642 removed outlier: 3.548A pdb=" N TYR B2634 " --> pdb=" O ASN B2630 " (cutoff:3.500A) Processing helix chain 'B' and resid 2647 through 2660 Processing helix chain 'B' and resid 2663 through 2668 Processing helix chain 'B' and resid 2671 through 2680 Processing helix chain 'B' and resid 2686 through 2693 removed outlier: 3.514A pdb=" N PHE B2693 " --> pdb=" O MET B2689 " (cutoff:3.500A) Processing helix chain 'B' and resid 2703 through 2720 removed outlier: 3.504A pdb=" N LEU B2707 " --> pdb=" O ASN B2703 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B2711 " --> pdb=" O LEU B2707 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG B2712 " --> pdb=" O LEU B2708 " (cutoff:3.500A) Processing helix chain 'B' and resid 2722 through 2735 Processing helix chain 'B' and resid 2779 through 2793 removed outlier: 3.911A pdb=" N THR B2793 " --> pdb=" O LEU B2789 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 3.686A pdb=" N SER A 843 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 872 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 841 " --> pdb=" O GLU A 872 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 53 removed outlier: 4.223A pdb=" N GLN A 50 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 53 removed outlier: 4.223A pdb=" N GLN A 50 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.741A pdb=" N CYS A 373 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 424 through 429 Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 478 removed outlier: 5.745A pdb=" N GLY A 495 " --> pdb=" O THR A 734 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A 734 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 547 through 550 Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 752 removed outlier: 6.770A pdb=" N VAL A 759 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL A 749 " --> pdb=" O HIS A 757 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N HIS A 757 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL A 751 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.256A pdb=" N LEU A 812 " --> pdb=" O TYR A 820 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1207 through 1208 Processing sheet with id=AB2, first strand: chain 'A' and resid 2242 through 2244 removed outlier: 3.591A pdb=" N THR A2280 " --> pdb=" O LEU A2242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2505 through 2506 Processing sheet with id=AB4, first strand: chain 'A' and resid 2603 through 2605 Processing sheet with id=AB5, first strand: chain 'A' and resid 2695 through 2698 removed outlier: 6.357A pdb=" N SER A2695 " --> pdb=" O ILE A2752 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE A2754 " --> pdb=" O SER A2695 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN A2697 " --> pdb=" O ILE A2754 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER A2751 " --> pdb=" O LEU A2772 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A2774 " --> pdb=" O SER A2751 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR A2753 " --> pdb=" O VAL A2774 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 2 through 10 removed outlier: 6.741A pdb=" N ALA B 864 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL B 848 " --> pdb=" O ALA B 864 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 866 " --> pdb=" O MET B 846 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N MET B 846 " --> pdb=" O VAL B 866 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 868 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 844 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA B 870 " --> pdb=" O SER B 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.542A pdb=" N GLN B 50 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.542A pdb=" N GLN B 50 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 373 through 376 removed outlier: 3.731A pdb=" N CYS B 373 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 424 through 429 Processing sheet with id=AC2, first strand: chain 'B' and resid 475 through 478 removed outlier: 4.554A pdb=" N LEU B 491 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY B 495 " --> pdb=" O THR B 734 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR B 734 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 546 through 550 removed outlier: 3.501A pdb=" N ALA B 546 " --> pdb=" O LEU B 561 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 745 through 751 removed outlier: 6.608A pdb=" N VAL B 759 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 749 " --> pdb=" O HIS B 757 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS B 757 " --> pdb=" O VAL B 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 800 through 802 removed outlier: 4.086A pdb=" N LEU B 812 " --> pdb=" O TYR B 820 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1194 through 1196 Processing sheet with id=AC7, first strand: chain 'B' and resid 2505 through 2506 Processing sheet with id=AC8, first strand: chain 'B' and resid 2603 through 2604 removed outlier: 3.563A pdb=" N VAL B2615 " --> pdb=" O ILE B2604 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 2695 through 2698 removed outlier: 6.495A pdb=" N SER B2751 " --> pdb=" O LEU B2772 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL B2774 " --> pdb=" O SER B2751 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N THR B2753 " --> pdb=" O VAL B2774 " (cutoff:3.500A) 1189 hydrogen bonds defined for protein. 3387 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: 18.16 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5046 1.33 - 1.45: 6348 1.45 - 1.57: 15462 1.57 - 1.69: 0 1.69 - 1.81: 296 Bond restraints: 27152 Sorted by residual: bond pdb=" CA SER B1933 " pdb=" CB SER B1933 " ideal model delta sigma weight residual 1.529 1.474 0.056 1.69e-02 3.50e+03 1.09e+01 bond pdb=" CA SER A1857 " pdb=" CB SER A1857 " ideal model delta sigma weight residual 1.528 1.479 0.050 1.56e-02 4.11e+03 1.02e+01 bond pdb=" CA SER B1857 " pdb=" CB SER B1857 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.56e-02 4.11e+03 9.14e+00 bond pdb=" C TYR B1855 " pdb=" O TYR B1855 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.17e-02 7.31e+03 7.39e+00 bond pdb=" C ALA B1851 " pdb=" O ALA B1851 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.17e-02 7.31e+03 7.31e+00 ... (remaining 27147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 36308 2.08 - 4.15: 432 4.15 - 6.23: 42 6.23 - 8.31: 4 8.31 - 10.39: 2 Bond angle restraints: 36788 Sorted by residual: angle pdb=" CG ARG A1854 " pdb=" CD ARG A1854 " pdb=" NE ARG A1854 " ideal model delta sigma weight residual 112.00 103.56 8.44 2.20e+00 2.07e-01 1.47e+01 angle pdb=" N GLU B1850 " pdb=" CA GLU B1850 " pdb=" C GLU B1850 " ideal model delta sigma weight residual 111.36 107.26 4.10 1.09e+00 8.42e-01 1.41e+01 angle pdb=" N ALA B1860 " pdb=" CA ALA B1860 " pdb=" C ALA B1860 " ideal model delta sigma weight residual 111.07 107.14 3.93 1.07e+00 8.73e-01 1.35e+01 angle pdb=" CA TYR A1855 " pdb=" CB TYR A1855 " pdb=" CG TYR A1855 " ideal model delta sigma weight residual 113.90 107.73 6.17 1.80e+00 3.09e-01 1.17e+01 angle pdb=" CA SER B1933 " pdb=" C SER B1933 " pdb=" O SER B1933 " ideal model delta sigma weight residual 121.19 117.63 3.56 1.10e+00 8.26e-01 1.05e+01 ... (remaining 36783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 15463 17.80 - 35.59: 911 35.59 - 53.39: 210 53.39 - 71.18: 40 71.18 - 88.98: 14 Dihedral angle restraints: 16638 sinusoidal: 6766 harmonic: 9872 Sorted by residual: dihedral pdb=" CA THR A2270 " pdb=" C THR A2270 " pdb=" N PRO A2271 " pdb=" CA PRO A2271 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" C ASP B1934 " pdb=" N ASP B1934 " pdb=" CA ASP B1934 " pdb=" CB ASP B1934 " ideal model delta harmonic sigma weight residual -122.60 -132.42 9.82 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" CA ILE B1453 " pdb=" C ILE B1453 " pdb=" N PRO B1454 " pdb=" CA PRO B1454 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 16635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3821 0.072 - 0.144: 315 0.144 - 0.217: 7 0.217 - 0.289: 0 0.289 - 0.361: 1 Chirality restraints: 4144 Sorted by residual: chirality pdb=" CA ASP B1934 " pdb=" N ASP B1934 " pdb=" C ASP B1934 " pdb=" CB ASP B1934 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA VAL B1935 " pdb=" N VAL B1935 " pdb=" C VAL B1935 " pdb=" CB VAL B1935 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU A 653 " pdb=" CB LEU A 653 " pdb=" CD1 LEU A 653 " pdb=" CD2 LEU A 653 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4141 not shown) Planarity restraints: 4762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A2270 " 0.060 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO A2271 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A2271 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A2271 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B1849 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C THR B1849 " 0.046 2.00e-02 2.50e+03 pdb=" O THR B1849 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU B1850 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1849 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C THR A1849 " -0.045 2.00e-02 2.50e+03 pdb=" O THR A1849 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A1850 " 0.015 2.00e-02 2.50e+03 ... (remaining 4759 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2868 2.74 - 3.28: 27206 3.28 - 3.82: 44213 3.82 - 4.36: 51143 4.36 - 4.90: 87897 Nonbonded interactions: 213327 Sorted by model distance: nonbonded pdb=" OG SER B 379 " pdb=" OE1 GLU B 380 " model vdw 2.205 3.040 nonbonded pdb=" O ASN B1962 " pdb=" OG1 THR B1965 " model vdw 2.222 3.040 nonbonded pdb=" O LYS A 370 " pdb=" OG SER A 386 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR B 14 " pdb=" OE1 GLN B 17 " model vdw 2.238 3.040 nonbonded pdb=" O LYS B 370 " pdb=" OG SER B 386 " model vdw 2.244 3.040 ... (remaining 213322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 82.470 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.140 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:58.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.004 0.056 27176 Z= 0.175 Angle : 0.546 10.385 36816 Z= 0.292 Chirality : 0.041 0.361 4144 Planarity : 0.005 0.091 4762 Dihedral : 12.185 88.981 10202 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.21 % Favored : 95.73 % Rotamer: Outliers : 4.74 % Allowed : 8.71 % Favored : 86.55 % 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: 0.46 (0.15), residues: 3326 helix: 1.33 (0.14), residues: 1424 sheet: 0.42 (0.31), residues: 306 loop : -0.63 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 393 HIS 0.005 0.001 HIS B1932 PHE 0.016 0.001 PHE A2746 TYR 0.032 0.002 TYR A1855 ARG 0.004 0.000 ARG A1854 Details of bonding type rmsd hydrogen bonds : bond 0.13715 ( 1175) hydrogen bonds : angle 5.27925 ( 3387) metal coordination : bond 0.00807 ( 24) metal coordination : angle 2.32302 ( 28) covalent geometry : bond 0.00357 (27152) covalent geometry : angle 0.54243 (36788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 728 time to evaluate : 2.674 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 17 GLN cc_start: 0.7564 (mp10) cc_final: 0.7093 (mp10) REVERT: A 75 GLN cc_start: 0.8018 (pm20) cc_final: 0.6723 (pp30) REVERT: A 361 GLN cc_start: 0.8336 (pt0) cc_final: 0.8055 (pt0) REVERT: A 482 TYR cc_start: 0.7454 (p90) cc_final: 0.7251 (p90) REVERT: A 494 TRP cc_start: 0.7716 (p-90) cc_final: 0.7457 (p-90) REVERT: A 736 LYS cc_start: 0.7983 (ptmm) cc_final: 0.7524 (ptpp) REVERT: A 745 GLU cc_start: 0.7632 (mp0) cc_final: 0.7404 (mp0) REVERT: A 762 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8422 (p) REVERT: A 834 ASP cc_start: 0.7783 (p0) cc_final: 0.7428 (p0) REVERT: A 876 LEU cc_start: 0.8122 (tp) cc_final: 0.7909 (tp) REVERT: A 889 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7863 (tmm-80) REVERT: A 890 GLN cc_start: 0.8148 (mm-40) cc_final: 0.6962 (mm-40) REVERT: A 893 MET cc_start: 0.8056 (mmm) cc_final: 0.7838 (mmm) REVERT: A 894 ASN cc_start: 0.8482 (m110) cc_final: 0.8181 (m110) REVERT: A 1090 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7960 (tppp) REVERT: A 1157 MET cc_start: 0.8780 (ptp) cc_final: 0.8529 (ptt) REVERT: A 1193 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8215 (mp) REVERT: A 1222 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7701 (mtmm) REVERT: A 1233 ASP cc_start: 0.7678 (p0) cc_final: 0.7308 (p0) REVERT: A 1254 LEU cc_start: 0.8499 (tp) cc_final: 0.8281 (tt) REVERT: A 1263 ASN cc_start: 0.7991 (p0) cc_final: 0.7713 (p0) REVERT: A 1314 MET cc_start: 0.6561 (ttp) cc_final: 0.6225 (ttp) REVERT: A 1505 ASP cc_start: 0.7789 (t0) cc_final: 0.7540 (t0) REVERT: A 1511 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 1957 TRP cc_start: 0.8533 (t-100) cc_final: 0.8280 (t-100) REVERT: A 2030 THR cc_start: 0.8096 (t) cc_final: 0.7887 (p) REVERT: A 2052 ASP cc_start: 0.7755 (t70) cc_final: 0.7360 (t70) REVERT: A 2072 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.5613 (pt0) REVERT: A 2086 MET cc_start: 0.1217 (ptp) cc_final: -0.1015 (ptp) REVERT: A 2102 MET cc_start: 0.2960 (ppp) cc_final: 0.2602 (pp-130) REVERT: A 2176 MET cc_start: 0.5913 (tpt) cc_final: 0.5695 (tpt) REVERT: A 2178 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7161 (pmm) REVERT: A 2211 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7905 (pp) REVERT: A 2219 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7532 (mp0) REVERT: A 2237 SER cc_start: 0.6639 (OUTLIER) cc_final: 0.5547 (t) REVERT: A 2517 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7716 (ttt90) REVERT: A 2520 LYS cc_start: 0.7715 (mttt) cc_final: 0.7331 (mttp) REVERT: A 2544 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 2633 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7228 (tm-30) REVERT: A 2637 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7699 (mttm) REVERT: A 2685 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8612 (p) REVERT: A 2689 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7140 (tpp) REVERT: A 2753 THR cc_start: 0.6713 (m) cc_final: 0.6458 (m) REVERT: A 2760 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6769 (pm20) REVERT: B 28 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8344 (ttmm) REVERT: B 44 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7007 (mm-30) REVERT: B 47 THR cc_start: 0.8826 (p) cc_final: 0.8608 (p) REVERT: B 63 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7117 (mp0) REVERT: B 501 GLN cc_start: 0.7833 (mt0) cc_final: 0.7443 (mt0) REVERT: B 505 MET cc_start: 0.6490 (mmm) cc_final: 0.6106 (mmm) REVERT: B 507 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: B 512 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.7012 (pttt) REVERT: B 655 GLU cc_start: 0.7740 (mp0) cc_final: 0.7538 (mp0) REVERT: B 834 ASP cc_start: 0.7558 (p0) cc_final: 0.7150 (p0) REVERT: B 884 ASP cc_start: 0.7932 (m-30) cc_final: 0.7721 (t0) REVERT: B 1090 LYS cc_start: 0.8559 (tppp) cc_final: 0.8177 (tppp) REVERT: B 1094 ASP cc_start: 0.7543 (m-30) cc_final: 0.7260 (m-30) REVERT: B 1152 ASP cc_start: 0.7684 (m-30) cc_final: 0.7437 (m-30) REVERT: B 1195 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: B 1222 LYS cc_start: 0.8340 (ptpt) cc_final: 0.8108 (mtpt) REVERT: B 1366 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5168 (tp30) REVERT: B 1511 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7130 (tm-30) REVERT: B 2026 SER cc_start: 0.8017 (p) cc_final: 0.7757 (t) REVERT: B 2027 ASP cc_start: 0.7699 (t0) cc_final: 0.7400 (t0) REVERT: B 2102 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5924 (pp-130) REVERT: B 2166 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8549 (tm) REVERT: B 2175 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7407 (t80) REVERT: B 2176 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5276 (ttp) REVERT: B 2178 MET cc_start: 0.7743 (ptm) cc_final: 0.7465 (ptm) REVERT: B 2225 PHE cc_start: 0.8513 (t80) cc_final: 0.8277 (t80) REVERT: B 2301 GLN cc_start: 0.8483 (tt0) cc_final: 0.8157 (mt0) REVERT: B 2562 LYS cc_start: 0.8429 (tmmm) cc_final: 0.8225 (ttpp) REVERT: B 2563 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8574 (m) REVERT: B 2572 ASP cc_start: 0.7346 (p0) cc_final: 0.6850 (p0) REVERT: B 2575 MET cc_start: 0.6844 (tpp) cc_final: 0.6510 (tpp) REVERT: B 2598 MET cc_start: 0.7232 (ptp) cc_final: 0.6985 (ptp) REVERT: B 2649 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7163 (pt0) REVERT: B 2664 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7761 (mmmm) REVERT: B 2708 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6630 (mm) REVERT: B 2723 MET cc_start: 0.7223 (tpp) cc_final: 0.6587 (tpp) REVERT: B 2743 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7663 (mt-10) outliers start: 141 outliers final: 52 residues processed: 826 average time/residue: 1.3532 time to fit residues: 1300.5983 Evaluate side-chains 698 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 624 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2178 MET Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2237 SER Chi-restraints excluded: chain A residue 2240 LEU Chi-restraints excluded: chain A residue 2245 ASP Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2517 ARG Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2623 ASN Chi-restraints excluded: chain A residue 2685 VAL Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2760 GLN Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 507 GLU Chi-restraints excluded: chain B residue 512 LYS Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1366 GLU Chi-restraints excluded: chain B residue 1404 THR Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1697 ARG Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1705 ASN Chi-restraints excluded: chain B residue 1718 VAL Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1933 SER Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 2102 MET Chi-restraints excluded: chain B residue 2166 LEU Chi-restraints excluded: chain B residue 2175 PHE Chi-restraints excluded: chain B residue 2176 MET Chi-restraints excluded: chain B residue 2295 PHE Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2548 ILE Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2600 LEU Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2707 LEU Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2722 SER Chi-restraints excluded: chain B residue 2724 THR Chi-restraints excluded: chain B residue 2762 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 141 optimal weight: 0.0050 chunk 86 optimal weight: 0.7980 chunk 171 optimal weight: 0.0070 chunk 136 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 101 optimal weight: 0.0060 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 overall best weight: 0.3228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 794 GLN A 924 HIS A1373 GLN A1411 ASN A1508 GLN A1720 ASN A1852 GLN A2253 GLN A2260 ASN A2262 HIS A2275 HIS ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2543 ASN A2587 GLN B 411 HIS B 421 ASN B 441 ASN B 469 GLN B 780 GLN B 782 ASN B 794 GLN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1334 GLN B1411 ASN B1705 ASN B1852 GLN B1932 HIS B1952 GLN B2020 HIS B2236 GLN ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2527 ASN B2542 GLN B2680 ASN B2727 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.161089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134588 restraints weight = 42733.134| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.51 r_work: 0.3746 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27176 Z= 0.131 Angle : 0.587 11.066 36816 Z= 0.293 Chirality : 0.040 0.181 4144 Planarity : 0.005 0.069 4762 Dihedral : 7.057 73.203 3779 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 4.94 % Allowed : 15.90 % Favored : 79.15 % 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: 0.64 (0.15), residues: 3326 helix: 1.53 (0.14), residues: 1424 sheet: 0.52 (0.30), residues: 304 loop : -0.59 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1235 HIS 0.010 0.001 HIS B1928 PHE 0.024 0.002 PHE A1087 TYR 0.021 0.001 TYR B 401 ARG 0.011 0.000 ARG B1854 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 1175) hydrogen bonds : angle 4.30666 ( 3387) metal coordination : bond 0.00566 ( 24) metal coordination : angle 2.16863 ( 28) covalent geometry : bond 0.00285 (27152) covalent geometry : angle 0.58392 (36788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 644 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7827 (mp10) cc_final: 0.7380 (mp10) REVERT: A 49 LYS cc_start: 0.8733 (tptt) cc_final: 0.8141 (tppp) REVERT: A 75 GLN cc_start: 0.7980 (pm20) cc_final: 0.6638 (pp30) REVERT: A 361 GLN cc_start: 0.8436 (pt0) cc_final: 0.8190 (pt0) REVERT: A 426 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6928 (mm) REVERT: A 433 ARG cc_start: 0.7351 (ttt90) cc_final: 0.6858 (ttm-80) REVERT: A 494 TRP cc_start: 0.7681 (p-90) cc_final: 0.7286 (p-90) REVERT: A 736 LYS cc_start: 0.8014 (ptmm) cc_final: 0.7451 (ptpp) REVERT: A 745 GLU cc_start: 0.7968 (mp0) cc_final: 0.7718 (mp0) REVERT: A 761 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7939 (tttp) REVERT: A 765 TRP cc_start: 0.7828 (t60) cc_final: 0.7546 (t60) REVERT: A 791 PHE cc_start: 0.8792 (t80) cc_final: 0.8526 (t80) REVERT: A 822 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8462 (mmp) REVERT: A 834 ASP cc_start: 0.8118 (p0) cc_final: 0.7760 (p0) REVERT: A 848 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7545 (t) REVERT: A 875 THR cc_start: 0.8030 (p) cc_final: 0.7770 (p) REVERT: A 889 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7911 (tmm-80) REVERT: A 890 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7149 (mm-40) REVERT: A 893 MET cc_start: 0.8481 (mmm) cc_final: 0.8101 (mmm) REVERT: A 894 ASN cc_start: 0.8535 (m110) cc_final: 0.8194 (m110) REVERT: A 1090 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7910 (tppp) REVERT: A 1222 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7836 (mtmm) REVERT: A 1233 ASP cc_start: 0.7786 (p0) cc_final: 0.7489 (p0) REVERT: A 1263 ASN cc_start: 0.8156 (p0) cc_final: 0.7910 (p0) REVERT: A 1314 MET cc_start: 0.6667 (ttp) cc_final: 0.6277 (ttp) REVERT: A 1505 ASP cc_start: 0.7723 (t0) cc_final: 0.7461 (t0) REVERT: A 1511 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7169 (tm-30) REVERT: A 1957 TRP cc_start: 0.8526 (t-100) cc_final: 0.8270 (t-100) REVERT: A 1959 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8200 (ttmm) REVERT: A 2052 ASP cc_start: 0.8234 (t70) cc_final: 0.7875 (t70) REVERT: A 2086 MET cc_start: 0.1676 (ptp) cc_final: -0.0334 (ptp) REVERT: A 2102 MET cc_start: 0.3153 (ppp) cc_final: 0.2753 (pp-130) REVERT: A 2176 MET cc_start: 0.6351 (tpt) cc_final: 0.6025 (tpt) REVERT: A 2211 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8002 (pp) REVERT: A 2219 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 2237 SER cc_start: 0.6929 (OUTLIER) cc_final: 0.5872 (m) REVERT: A 2520 LYS cc_start: 0.7722 (mttt) cc_final: 0.7441 (mttt) REVERT: A 2544 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 2575 MET cc_start: 0.8335 (tpp) cc_final: 0.8118 (tpt) REVERT: A 2618 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8614 (mm) REVERT: A 2630 ASN cc_start: 0.8301 (t0) cc_final: 0.8083 (t0) REVERT: A 2674 ASP cc_start: 0.7885 (m-30) cc_final: 0.7661 (m-30) REVERT: A 2685 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 2689 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7579 (tpp) REVERT: A 2753 THR cc_start: 0.6715 (m) cc_final: 0.6162 (p) REVERT: B 1 MET cc_start: 0.8432 (tpp) cc_final: 0.8204 (tpp) REVERT: B 2 THR cc_start: 0.8286 (t) cc_final: 0.7252 (p) REVERT: B 21 ARG cc_start: 0.8422 (mmp80) cc_final: 0.8171 (mmp80) REVERT: B 28 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8465 (ttmm) REVERT: B 44 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7019 (mm-30) REVERT: B 47 THR cc_start: 0.8870 (p) cc_final: 0.8631 (p) REVERT: B 63 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7486 (mp0) REVERT: B 457 LYS cc_start: 0.7479 (ptpt) cc_final: 0.7237 (ptpt) REVERT: B 501 GLN cc_start: 0.7943 (mt0) cc_final: 0.7607 (mt0) REVERT: B 505 MET cc_start: 0.7166 (mmm) cc_final: 0.6710 (mmm) REVERT: B 563 GLU cc_start: 0.7154 (pp20) cc_final: 0.6903 (pp20) REVERT: B 655 GLU cc_start: 0.7975 (mp0) cc_final: 0.7721 (mp0) REVERT: B 659 VAL cc_start: 0.8666 (m) cc_final: 0.8387 (p) REVERT: B 834 ASP cc_start: 0.7907 (p0) cc_final: 0.7521 (p0) REVERT: B 872 GLU cc_start: 0.7867 (mp0) cc_final: 0.7404 (mp0) REVERT: B 884 ASP cc_start: 0.8028 (m-30) cc_final: 0.7690 (t0) REVERT: B 1082 LYS cc_start: 0.7799 (pptt) cc_final: 0.7568 (pptt) REVERT: B 1090 LYS cc_start: 0.8663 (tppp) cc_final: 0.8350 (tppp) REVERT: B 1094 ASP cc_start: 0.7803 (m-30) cc_final: 0.7531 (m-30) REVERT: B 1148 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 1462 ARG cc_start: 0.8492 (mtp180) cc_final: 0.8250 (ttm170) REVERT: B 1511 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7288 (tm-30) REVERT: B 1823 ASP cc_start: 0.7455 (m-30) cc_final: 0.7246 (m-30) REVERT: B 1825 VAL cc_start: 0.8471 (t) cc_final: 0.8144 (m) REVERT: B 1833 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: B 1929 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7390 (p0) REVERT: B 1931 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: B 2026 SER cc_start: 0.8090 (p) cc_final: 0.7835 (t) REVERT: B 2027 ASP cc_start: 0.7827 (t0) cc_final: 0.7485 (t0) REVERT: B 2086 MET cc_start: 0.7021 (ptm) cc_final: 0.6818 (ptm) REVERT: B 2102 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.6160 (pp-130) REVERT: B 2166 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8525 (tm) REVERT: B 2176 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5510 (ttp) REVERT: B 2221 LYS cc_start: 0.8423 (mtpp) cc_final: 0.8138 (mtmm) REVERT: B 2248 ARG cc_start: 0.7294 (mpp-170) cc_final: 0.7034 (mpp-170) REVERT: B 2301 GLN cc_start: 0.8669 (tt0) cc_final: 0.8410 (mt0) REVERT: B 2562 LYS cc_start: 0.8550 (tmmm) cc_final: 0.8345 (ttpp) REVERT: B 2563 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8555 (m) REVERT: B 2565 TRP cc_start: 0.8163 (t60) cc_final: 0.7601 (t60) REVERT: B 2575 MET cc_start: 0.7309 (tpp) cc_final: 0.7019 (tpp) REVERT: B 2598 MET cc_start: 0.7347 (ptp) cc_final: 0.7091 (ptp) REVERT: B 2649 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7324 (pt0) REVERT: B 2674 ASP cc_start: 0.7871 (m-30) cc_final: 0.7340 (m-30) REVERT: B 2708 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6569 (mm) REVERT: B 2723 MET cc_start: 0.7509 (tpp) cc_final: 0.6795 (tpp) REVERT: B 2743 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8218 (mt-10) outliers start: 147 outliers final: 67 residues processed: 733 average time/residue: 1.3239 time to fit residues: 1129.9330 Evaluate side-chains 693 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 607 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1818 LYS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2057 LEU Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2237 SER Chi-restraints excluded: chain A residue 2240 LEU Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2618 ILE Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2685 VAL Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2690 LEU Chi-restraints excluded: chain A residue 2708 LEU Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1833 GLU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1929 ASN Chi-restraints excluded: chain B residue 1931 GLU Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2102 MET Chi-restraints excluded: chain B residue 2166 LEU Chi-restraints excluded: chain B residue 2176 MET Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2600 LEU Chi-restraints excluded: chain B residue 2618 ILE Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2707 LEU Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2724 THR Chi-restraints excluded: chain B residue 2762 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 121 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 65 optimal weight: 0.0370 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 325 optimal weight: 2.9990 chunk 260 optimal weight: 0.0170 chunk 160 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 ASN A 914 HIS A1373 GLN A1411 ASN A1720 ASN A1962 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 794 GLN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS B1952 GLN ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.162496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.136278 restraints weight = 42639.623| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.48 r_work: 0.3759 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27176 Z= 0.115 Angle : 0.572 10.996 36816 Z= 0.284 Chirality : 0.040 0.195 4144 Planarity : 0.004 0.062 4762 Dihedral : 6.110 57.637 3726 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.46 % Rotamer: Outliers : 5.08 % Allowed : 17.11 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3326 helix: 1.60 (0.14), residues: 1422 sheet: 0.59 (0.30), residues: 304 loop : -0.60 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1235 HIS 0.004 0.001 HIS A2553 PHE 0.034 0.001 PHE A1087 TYR 0.021 0.001 TYR A2506 ARG 0.008 0.000 ARG A2257 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 1175) hydrogen bonds : angle 4.12257 ( 3387) metal coordination : bond 0.00401 ( 24) metal coordination : angle 1.90335 ( 28) covalent geometry : bond 0.00259 (27152) covalent geometry : angle 0.56984 (36788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 640 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7870 (mp10) cc_final: 0.7370 (mp10) REVERT: A 49 LYS cc_start: 0.8724 (tptt) cc_final: 0.8126 (tppp) REVERT: A 57 HIS cc_start: 0.7175 (m-70) cc_final: 0.6950 (m-70) REVERT: A 75 GLN cc_start: 0.7981 (pm20) cc_final: 0.6721 (pp30) REVERT: A 361 GLN cc_start: 0.8353 (pt0) cc_final: 0.8045 (pt0) REVERT: A 426 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6898 (mm) REVERT: A 433 ARG cc_start: 0.7319 (ttt90) cc_final: 0.6836 (ttt90) REVERT: A 494 TRP cc_start: 0.7654 (p-90) cc_final: 0.7266 (p-90) REVERT: A 736 LYS cc_start: 0.8005 (ptmm) cc_final: 0.7417 (ptpp) REVERT: A 745 GLU cc_start: 0.7946 (mp0) cc_final: 0.7712 (mp0) REVERT: A 761 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7950 (tttp) REVERT: A 765 TRP cc_start: 0.7838 (t60) cc_final: 0.7578 (t60) REVERT: A 827 MET cc_start: 0.8135 (mmm) cc_final: 0.7786 (mmm) REVERT: A 834 ASP cc_start: 0.8118 (p0) cc_final: 0.7658 (p0) REVERT: A 848 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7592 (t) REVERT: A 872 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7227 (mp0) REVERT: A 875 THR cc_start: 0.7993 (p) cc_final: 0.7706 (p) REVERT: A 889 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8016 (tmm-80) REVERT: A 893 MET cc_start: 0.8484 (mmm) cc_final: 0.8153 (mmm) REVERT: A 894 ASN cc_start: 0.8532 (m110) cc_final: 0.8131 (m110) REVERT: A 1090 LYS cc_start: 0.8313 (ttmm) cc_final: 0.7895 (tppp) REVERT: A 1193 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8322 (mp) REVERT: A 1222 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7951 (mtmm) REVERT: A 1263 ASN cc_start: 0.8140 (p0) cc_final: 0.7884 (p0) REVERT: A 1314 MET cc_start: 0.6674 (ttp) cc_final: 0.6267 (ttp) REVERT: A 1505 ASP cc_start: 0.7707 (t0) cc_final: 0.7464 (t0) REVERT: A 1511 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 1959 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8233 (ttmm) REVERT: A 2052 ASP cc_start: 0.8218 (t70) cc_final: 0.7886 (t70) REVERT: A 2072 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.5839 (pt0) REVERT: A 2086 MET cc_start: 0.1420 (ptp) cc_final: -0.0527 (ptp) REVERT: A 2091 ASP cc_start: 0.7770 (p0) cc_final: 0.7551 (p0) REVERT: A 2102 MET cc_start: 0.3174 (ppp) cc_final: 0.2786 (pp-130) REVERT: A 2176 MET cc_start: 0.6257 (tpt) cc_final: 0.5995 (tpt) REVERT: A 2211 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8020 (pp) REVERT: A 2219 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 2237 SER cc_start: 0.6699 (OUTLIER) cc_final: 0.5736 (m) REVERT: A 2246 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7470 (tpp80) REVERT: A 2520 LYS cc_start: 0.7742 (mttt) cc_final: 0.7344 (mptt) REVERT: A 2544 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7649 (mm-30) REVERT: A 2630 ASN cc_start: 0.8292 (t0) cc_final: 0.8016 (t0) REVERT: A 2634 TYR cc_start: 0.8334 (t80) cc_final: 0.7956 (t80) REVERT: A 2674 ASP cc_start: 0.7932 (m-30) cc_final: 0.7681 (m-30) REVERT: A 2685 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8750 (p) REVERT: A 2689 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7524 (tpp) REVERT: A 2753 THR cc_start: 0.6686 (m) cc_final: 0.6220 (p) REVERT: A 2774 VAL cc_start: 0.8477 (m) cc_final: 0.8212 (p) REVERT: A 2777 TYR cc_start: 0.8097 (m-10) cc_final: 0.7892 (m-10) REVERT: B 1 MET cc_start: 0.8423 (tpp) cc_final: 0.8144 (tpp) REVERT: B 2 THR cc_start: 0.8282 (t) cc_final: 0.7249 (m) REVERT: B 28 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8486 (ttmm) REVERT: B 44 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6984 (mm-30) REVERT: B 501 GLN cc_start: 0.7947 (mt0) cc_final: 0.7597 (mt0) REVERT: B 505 MET cc_start: 0.7176 (mmm) cc_final: 0.6684 (mmm) REVERT: B 507 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 563 GLU cc_start: 0.7142 (pp20) cc_final: 0.6830 (pp20) REVERT: B 649 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6701 (tm-30) REVERT: B 651 TRP cc_start: 0.8482 (m-10) cc_final: 0.8183 (m-10) REVERT: B 834 ASP cc_start: 0.7920 (p0) cc_final: 0.7561 (p0) REVERT: B 872 GLU cc_start: 0.7906 (mp0) cc_final: 0.7403 (mp0) REVERT: B 885 TYR cc_start: 0.8455 (t80) cc_final: 0.8148 (t80) REVERT: B 1082 LYS cc_start: 0.7808 (pptt) cc_final: 0.7597 (pptt) REVERT: B 1090 LYS cc_start: 0.8661 (tppp) cc_final: 0.8330 (tppp) REVERT: B 1094 ASP cc_start: 0.7823 (m-30) cc_final: 0.7530 (m-30) REVERT: B 1143 GLU cc_start: 0.7271 (tp30) cc_final: 0.7036 (tp30) REVERT: B 1148 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8020 (mm-30) REVERT: B 1152 ASP cc_start: 0.8209 (m-30) cc_final: 0.7946 (m-30) REVERT: B 1167 ASP cc_start: 0.8144 (m-30) cc_final: 0.7878 (m-30) REVERT: B 1511 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 1823 ASP cc_start: 0.7441 (m-30) cc_final: 0.7197 (m-30) REVERT: B 1833 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: B 1929 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7412 (p0) REVERT: B 1959 LYS cc_start: 0.8431 (ttmm) cc_final: 0.8150 (ttmm) REVERT: B 2027 ASP cc_start: 0.7821 (t0) cc_final: 0.7498 (t0) REVERT: B 2166 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8522 (tm) REVERT: B 2221 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8060 (mtmm) REVERT: B 2301 GLN cc_start: 0.8627 (tt0) cc_final: 0.8369 (mt0) REVERT: B 2303 PHE cc_start: 0.8544 (m-80) cc_final: 0.8255 (m-80) REVERT: B 2562 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8322 (ttpp) REVERT: B 2563 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8515 (m) REVERT: B 2565 TRP cc_start: 0.8158 (t60) cc_final: 0.7584 (t60) REVERT: B 2575 MET cc_start: 0.7282 (tpp) cc_final: 0.6974 (tpp) REVERT: B 2598 MET cc_start: 0.7311 (ptp) cc_final: 0.7090 (ptp) REVERT: B 2649 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7290 (pt0) REVERT: B 2674 ASP cc_start: 0.7849 (m-30) cc_final: 0.7320 (m-30) REVERT: B 2708 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6582 (mm) REVERT: B 2723 MET cc_start: 0.7520 (tpp) cc_final: 0.6809 (tpp) REVERT: B 2743 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8279 (mt-10) outliers start: 151 outliers final: 77 residues processed: 724 average time/residue: 1.3440 time to fit residues: 1134.4295 Evaluate side-chains 696 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 602 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1411 ASN Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1818 LYS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2057 LEU Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2237 SER Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2685 VAL Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1331 ARG Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1833 GLU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1929 ASN Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2166 LEU Chi-restraints excluded: chain B residue 2176 MET Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2548 ILE Chi-restraints excluded: chain B residue 2558 LEU Chi-restraints excluded: chain B residue 2562 LYS Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2600 LEU Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2707 LEU Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2724 THR Chi-restraints excluded: chain B residue 2762 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 203 optimal weight: 0.1980 chunk 23 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 285 optimal weight: 0.0170 chunk 327 optimal weight: 8.9990 chunk 335 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 GLN A1411 ASN A1720 ASN A1962 ASN A2262 HIS A2527 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B 489 ASN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS B1952 GLN ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2614 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.161168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.135252 restraints weight = 42989.701| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.47 r_work: 0.3752 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27176 Z= 0.128 Angle : 0.589 11.020 36816 Z= 0.289 Chirality : 0.040 0.191 4144 Planarity : 0.004 0.060 4762 Dihedral : 5.976 59.356 3717 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 5.62 % Allowed : 17.85 % Favored : 76.53 % 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: 0.67 (0.15), residues: 3326 helix: 1.61 (0.14), residues: 1424 sheet: 0.33 (0.29), residues: 328 loop : -0.59 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1235 HIS 0.005 0.001 HIS B1946 PHE 0.038 0.001 PHE A1087 TYR 0.019 0.001 TYR A1370 ARG 0.008 0.000 ARG B2233 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 1175) hydrogen bonds : angle 4.06010 ( 3387) metal coordination : bond 0.00572 ( 24) metal coordination : angle 2.17290 ( 28) covalent geometry : bond 0.00297 (27152) covalent geometry : angle 0.58659 (36788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 631 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7894 (mp10) cc_final: 0.7203 (mp10) REVERT: A 49 LYS cc_start: 0.8706 (tptt) cc_final: 0.8107 (tppp) REVERT: A 57 HIS cc_start: 0.7212 (m-70) cc_final: 0.6914 (m-70) REVERT: A 75 GLN cc_start: 0.7998 (pm20) cc_final: 0.6761 (pp30) REVERT: A 361 GLN cc_start: 0.8284 (pt0) cc_final: 0.7979 (pt0) REVERT: A 392 GLN cc_start: 0.7787 (pp30) cc_final: 0.7153 (pt0) REVERT: A 426 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6883 (mm) REVERT: A 433 ARG cc_start: 0.7321 (ttt90) cc_final: 0.6854 (ttt90) REVERT: A 494 TRP cc_start: 0.7680 (p-90) cc_final: 0.7286 (p-90) REVERT: A 736 LYS cc_start: 0.8018 (ptmm) cc_final: 0.7425 (ptpp) REVERT: A 745 GLU cc_start: 0.7980 (mp0) cc_final: 0.7743 (mp0) REVERT: A 761 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8013 (tttp) REVERT: A 822 MET cc_start: 0.8702 (tpp) cc_final: 0.8210 (mmt) REVERT: A 827 MET cc_start: 0.8131 (mmm) cc_final: 0.7780 (mmm) REVERT: A 834 ASP cc_start: 0.8124 (p0) cc_final: 0.7657 (p0) REVERT: A 848 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7601 (t) REVERT: A 872 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7262 (mp0) REVERT: A 875 THR cc_start: 0.7924 (p) cc_final: 0.7659 (p) REVERT: A 889 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8017 (tmm-80) REVERT: A 893 MET cc_start: 0.8496 (mmm) cc_final: 0.8188 (mmm) REVERT: A 894 ASN cc_start: 0.8545 (m110) cc_final: 0.8188 (m110) REVERT: A 1090 LYS cc_start: 0.8292 (ttmm) cc_final: 0.7905 (tppp) REVERT: A 1222 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7881 (mtmm) REVERT: A 1263 ASN cc_start: 0.8155 (p0) cc_final: 0.7891 (p0) REVERT: A 1314 MET cc_start: 0.6646 (ttp) cc_final: 0.6240 (ttp) REVERT: A 1505 ASP cc_start: 0.7746 (t0) cc_final: 0.7509 (t0) REVERT: A 1511 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 1959 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8227 (ttmm) REVERT: A 2052 ASP cc_start: 0.8185 (t70) cc_final: 0.7863 (t70) REVERT: A 2072 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6567 (pt0) REVERT: A 2091 ASP cc_start: 0.7830 (p0) cc_final: 0.7606 (p0) REVERT: A 2102 MET cc_start: 0.3234 (ppp) cc_final: 0.2835 (pp-130) REVERT: A 2176 MET cc_start: 0.6208 (tpt) cc_final: 0.5947 (tpt) REVERT: A 2211 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8053 (pp) REVERT: A 2246 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7500 (tpp80) REVERT: A 2520 LYS cc_start: 0.7765 (mttt) cc_final: 0.7311 (mttp) REVERT: A 2616 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 2630 ASN cc_start: 0.8301 (t0) cc_final: 0.8009 (t0) REVERT: A 2674 ASP cc_start: 0.7944 (m-30) cc_final: 0.7715 (m-30) REVERT: A 2685 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8769 (p) REVERT: A 2753 THR cc_start: 0.6764 (m) cc_final: 0.6269 (p) REVERT: A 2774 VAL cc_start: 0.8495 (m) cc_final: 0.8202 (p) REVERT: A 2777 TYR cc_start: 0.8074 (m-10) cc_final: 0.7863 (m-10) REVERT: B 2 THR cc_start: 0.8299 (t) cc_final: 0.7342 (m) REVERT: B 28 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8511 (ttmm) REVERT: B 44 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6988 (mm-30) REVERT: B 63 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7583 (mp0) REVERT: B 393 TRP cc_start: 0.7719 (p-90) cc_final: 0.7447 (p-90) REVERT: B 457 LYS cc_start: 0.7216 (ptpt) cc_final: 0.6729 (ptpt) REVERT: B 501 GLN cc_start: 0.7932 (mt0) cc_final: 0.7590 (mt0) REVERT: B 505 MET cc_start: 0.7183 (mmm) cc_final: 0.6692 (mmm) REVERT: B 507 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7884 (mm-30) REVERT: B 563 GLU cc_start: 0.7161 (pp20) cc_final: 0.6937 (pp20) REVERT: B 659 VAL cc_start: 0.8651 (m) cc_final: 0.8437 (p) REVERT: B 834 ASP cc_start: 0.7928 (p0) cc_final: 0.7602 (p0) REVERT: B 836 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8540 (mt) REVERT: B 885 TYR cc_start: 0.8510 (t80) cc_final: 0.8230 (t80) REVERT: B 889 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7424 (mtm-85) REVERT: B 1090 LYS cc_start: 0.8687 (tppp) cc_final: 0.8249 (tppp) REVERT: B 1094 ASP cc_start: 0.7800 (m-30) cc_final: 0.7467 (m-30) REVERT: B 1143 GLU cc_start: 0.7256 (tp30) cc_final: 0.6958 (tp30) REVERT: B 1167 ASP cc_start: 0.8139 (m-30) cc_final: 0.7874 (m-30) REVERT: B 1480 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7475 (tm-30) REVERT: B 1511 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 1823 ASP cc_start: 0.7469 (m-30) cc_final: 0.7217 (m-30) REVERT: B 1825 VAL cc_start: 0.8452 (t) cc_final: 0.8117 (m) REVERT: B 1833 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: B 1929 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7482 (p0) REVERT: B 2027 ASP cc_start: 0.7830 (t0) cc_final: 0.7526 (t0) REVERT: B 2069 ARG cc_start: 0.7649 (mtp-110) cc_final: 0.7334 (mtp180) REVERT: B 2166 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8506 (tm) REVERT: B 2221 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8075 (mtmm) REVERT: B 2225 PHE cc_start: 0.8488 (t80) cc_final: 0.8236 (t80) REVERT: B 2301 GLN cc_start: 0.8605 (tt0) cc_final: 0.8357 (mt0) REVERT: B 2543 ASN cc_start: 0.8332 (t0) cc_final: 0.8124 (t0) REVERT: B 2562 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8325 (ttpp) REVERT: B 2563 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8524 (m) REVERT: B 2564 ASN cc_start: 0.8427 (p0) cc_final: 0.8149 (p0) REVERT: B 2565 TRP cc_start: 0.8171 (t60) cc_final: 0.7572 (t60) REVERT: B 2575 MET cc_start: 0.7328 (tpp) cc_final: 0.6999 (tpp) REVERT: B 2598 MET cc_start: 0.7349 (ptp) cc_final: 0.7142 (ptp) REVERT: B 2649 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: B 2674 ASP cc_start: 0.7876 (m-30) cc_final: 0.7362 (m-30) REVERT: B 2708 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6584 (mm) REVERT: B 2723 MET cc_start: 0.7510 (tpp) cc_final: 0.6632 (tpp) REVERT: B 2743 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8294 (mt-10) outliers start: 167 outliers final: 85 residues processed: 727 average time/residue: 1.4421 time to fit residues: 1218.8746 Evaluate side-chains 708 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 607 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1411 ASN Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1719 ARG Chi-restraints excluded: chain A residue 1818 LYS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2057 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain A residue 2166 LEU Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2568 PHE Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2685 VAL Chi-restraints excluded: chain A residue 2746 PHE Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 889 ARG Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1405 LEU Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1833 GLU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1929 ASN Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2166 LEU Chi-restraints excluded: chain B residue 2176 MET Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2548 ILE Chi-restraints excluded: chain B residue 2562 LYS Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2600 LEU Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2707 LEU Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2724 THR Chi-restraints excluded: chain B residue 2762 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 276 optimal weight: 0.0010 chunk 282 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 237 optimal weight: 0.5980 chunk 259 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 ASN ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1720 ASN A1928 HIS A1962 ASN A2262 HIS ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2587 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS B1952 GLN ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.161521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.134937 restraints weight = 42910.107| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.53 r_work: 0.3750 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27176 Z= 0.126 Angle : 0.595 11.327 36816 Z= 0.292 Chirality : 0.041 0.225 4144 Planarity : 0.004 0.060 4762 Dihedral : 5.733 54.931 3711 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 5.51 % Allowed : 18.33 % Favored : 76.16 % 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: 0.67 (0.15), residues: 3326 helix: 1.61 (0.14), residues: 1436 sheet: 0.34 (0.29), residues: 328 loop : -0.61 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1235 HIS 0.004 0.001 HIS B1946 PHE 0.028 0.001 PHE A1087 TYR 0.023 0.001 TYR A2506 ARG 0.009 0.000 ARG A2755 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1175) hydrogen bonds : angle 4.02066 ( 3387) metal coordination : bond 0.00593 ( 24) metal coordination : angle 2.22375 ( 28) covalent geometry : bond 0.00294 (27152) covalent geometry : angle 0.59251 (36788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 635 time to evaluate : 2.858 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 17 GLN cc_start: 0.7915 (mp10) cc_final: 0.7219 (mp10) REVERT: A 49 LYS cc_start: 0.8712 (tptt) cc_final: 0.8210 (mmmm) REVERT: A 57 HIS cc_start: 0.7209 (m-70) cc_final: 0.6932 (m-70) REVERT: A 75 GLN cc_start: 0.7954 (pm20) cc_final: 0.6784 (pp30) REVERT: A 361 GLN cc_start: 0.8245 (pt0) cc_final: 0.7902 (pt0) REVERT: A 426 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6872 (mm) REVERT: A 433 ARG cc_start: 0.7282 (ttt90) cc_final: 0.6870 (ttt90) REVERT: A 494 TRP cc_start: 0.7668 (p-90) cc_final: 0.7295 (p-90) REVERT: A 736 LYS cc_start: 0.8025 (ptmm) cc_final: 0.7440 (ptpp) REVERT: A 745 GLU cc_start: 0.7956 (mp0) cc_final: 0.7712 (mp0) REVERT: A 761 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8001 (tttp) REVERT: A 827 MET cc_start: 0.8139 (mmm) cc_final: 0.7808 (mmm) REVERT: A 848 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7622 (t) REVERT: A 872 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7455 (mp0) REVERT: A 875 THR cc_start: 0.7932 (p) cc_final: 0.7662 (p) REVERT: A 889 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7924 (tmm-80) REVERT: A 890 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7166 (mm-40) REVERT: A 893 MET cc_start: 0.8470 (mmm) cc_final: 0.8156 (mmm) REVERT: A 894 ASN cc_start: 0.8545 (m110) cc_final: 0.8198 (m110) REVERT: A 1090 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7894 (tppp) REVERT: A 1103 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7594 (tmt170) REVERT: A 1222 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7870 (mmmm) REVERT: A 1263 ASN cc_start: 0.8164 (p0) cc_final: 0.7895 (p0) REVERT: A 1314 MET cc_start: 0.6641 (ttp) cc_final: 0.6235 (ttp) REVERT: A 1505 ASP cc_start: 0.7725 (t0) cc_final: 0.7511 (t0) REVERT: A 1511 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 1959 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8211 (ttmm) REVERT: A 2052 ASP cc_start: 0.8210 (t70) cc_final: 0.7923 (t70) REVERT: A 2072 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6271 (pt0) REVERT: A 2102 MET cc_start: 0.3313 (ppp) cc_final: 0.2889 (pp-130) REVERT: A 2176 MET cc_start: 0.6275 (tpt) cc_final: 0.6048 (tpt) REVERT: A 2178 MET cc_start: 0.7394 (pmm) cc_final: 0.7110 (pmt) REVERT: A 2211 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8075 (pp) REVERT: A 2219 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7889 (mp0) REVERT: A 2246 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7556 (tpp80) REVERT: A 2520 LYS cc_start: 0.7744 (mttt) cc_final: 0.7480 (mttt) REVERT: A 2544 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 2616 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7670 (mt-10) REVERT: A 2618 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8638 (mp) REVERT: A 2630 ASN cc_start: 0.8333 (t0) cc_final: 0.8012 (t0) REVERT: A 2674 ASP cc_start: 0.7952 (m-30) cc_final: 0.7727 (m-30) REVERT: A 2685 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8783 (p) REVERT: A 2753 THR cc_start: 0.6771 (m) cc_final: 0.6269 (p) REVERT: A 2774 VAL cc_start: 0.8505 (m) cc_final: 0.8208 (p) REVERT: B 2 THR cc_start: 0.8279 (t) cc_final: 0.7357 (m) REVERT: B 27 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 28 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8438 (ttmm) REVERT: B 44 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7070 (mm-30) REVERT: B 63 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7574 (mp0) REVERT: B 393 TRP cc_start: 0.7729 (p-90) cc_final: 0.7455 (p-90) REVERT: B 501 GLN cc_start: 0.7951 (mt0) cc_final: 0.7617 (mt0) REVERT: B 505 MET cc_start: 0.7178 (mmm) cc_final: 0.6665 (mmm) REVERT: B 563 GLU cc_start: 0.7178 (pp20) cc_final: 0.6825 (pp20) REVERT: B 834 ASP cc_start: 0.7965 (p0) cc_final: 0.7633 (p0) REVERT: B 836 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8534 (mt) REVERT: B 885 TYR cc_start: 0.8534 (t80) cc_final: 0.8254 (t80) REVERT: B 886 GLU cc_start: 0.7663 (mm-30) cc_final: 0.6482 (mm-30) REVERT: B 889 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7616 (mtm-85) REVERT: B 1082 LYS cc_start: 0.7824 (pptt) cc_final: 0.7593 (pptt) REVERT: B 1090 LYS cc_start: 0.8668 (tppp) cc_final: 0.8166 (tppp) REVERT: B 1094 ASP cc_start: 0.7801 (m-30) cc_final: 0.7439 (m-30) REVERT: B 1143 GLU cc_start: 0.7321 (tp30) cc_final: 0.6998 (tp30) REVERT: B 1263 ASN cc_start: 0.8201 (p0) cc_final: 0.7917 (p0) REVERT: B 1511 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 1691 LEU cc_start: 0.0843 (OUTLIER) cc_final: -0.0592 (mt) REVERT: B 1823 ASP cc_start: 0.7504 (m-30) cc_final: 0.7250 (m-30) REVERT: B 1833 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: B 1931 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: B 2166 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8521 (tm) REVERT: B 2221 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8058 (mtmm) REVERT: B 2225 PHE cc_start: 0.8463 (t80) cc_final: 0.8159 (t80) REVERT: B 2301 GLN cc_start: 0.8617 (tt0) cc_final: 0.8387 (mt0) REVERT: B 2543 ASN cc_start: 0.8332 (t0) cc_final: 0.8129 (t0) REVERT: B 2562 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8324 (ttpp) REVERT: B 2563 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8542 (m) REVERT: B 2564 ASN cc_start: 0.8448 (p0) cc_final: 0.8175 (p0) REVERT: B 2565 TRP cc_start: 0.8171 (t60) cc_final: 0.7568 (t60) REVERT: B 2575 MET cc_start: 0.7291 (tpp) cc_final: 0.6970 (tpp) REVERT: B 2649 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7304 (pt0) REVERT: B 2674 ASP cc_start: 0.7947 (m-30) cc_final: 0.7427 (m-30) REVERT: B 2708 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6523 (mm) REVERT: B 2723 MET cc_start: 0.7558 (tpp) cc_final: 0.6684 (tpp) REVERT: B 2743 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8284 (mt-10) outliers start: 164 outliers final: 93 residues processed: 733 average time/residue: 1.3710 time to fit residues: 1172.1330 Evaluate side-chains 716 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 604 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1103 ARG Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1818 LYS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2057 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain A residue 2166 LEU Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2618 ILE Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2685 VAL Chi-restraints excluded: chain A residue 2708 LEU Chi-restraints excluded: chain A residue 2746 PHE Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 889 ARG Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1339 LEU Chi-restraints excluded: chain B residue 1405 LEU Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1691 LEU Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1833 GLU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1931 GLU Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2166 LEU Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2548 ILE Chi-restraints excluded: chain B residue 2562 LYS Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2600 LEU Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2724 THR Chi-restraints excluded: chain B residue 2762 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 244 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 43 optimal weight: 0.0020 chunk 315 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 151 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 233 optimal weight: 0.7980 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 ASN A1411 ASN A1720 ASN A1962 ASN A2262 HIS A2527 ASN A2542 GLN A2587 GLN B 361 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 477 HIS B 489 ASN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN ** B1929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.162454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.136300 restraints weight = 42600.508| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.48 r_work: 0.3758 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27176 Z= 0.123 Angle : 0.606 10.407 36816 Z= 0.296 Chirality : 0.041 0.226 4144 Planarity : 0.004 0.060 4762 Dihedral : 5.591 56.240 3706 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 5.48 % Allowed : 19.70 % Favored : 74.82 % 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: 0.69 (0.15), residues: 3326 helix: 1.61 (0.14), residues: 1444 sheet: 0.53 (0.31), residues: 294 loop : -0.62 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1235 HIS 0.008 0.001 HIS B 460 PHE 0.028 0.001 PHE B2675 TYR 0.014 0.001 TYR A1855 ARG 0.009 0.000 ARG A1712 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 1175) hydrogen bonds : angle 3.99159 ( 3387) metal coordination : bond 0.00540 ( 24) metal coordination : angle 2.19635 ( 28) covalent geometry : bond 0.00287 (27152) covalent geometry : angle 0.60311 (36788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 630 time to evaluate : 2.800 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 17 GLN cc_start: 0.7910 (mp10) cc_final: 0.7220 (mp10) REVERT: A 49 LYS cc_start: 0.8714 (tptt) cc_final: 0.8218 (mmmm) REVERT: A 57 HIS cc_start: 0.7182 (m-70) cc_final: 0.6896 (m-70) REVERT: A 75 GLN cc_start: 0.7920 (pm20) cc_final: 0.6801 (pp30) REVERT: A 361 GLN cc_start: 0.8197 (pt0) cc_final: 0.7886 (pt0) REVERT: A 392 GLN cc_start: 0.7802 (pp30) cc_final: 0.7080 (pt0) REVERT: A 426 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6907 (mm) REVERT: A 494 TRP cc_start: 0.7656 (p-90) cc_final: 0.7370 (p-90) REVERT: A 736 LYS cc_start: 0.8038 (ptmm) cc_final: 0.7444 (ptpp) REVERT: A 745 GLU cc_start: 0.7926 (mp0) cc_final: 0.7702 (mp0) REVERT: A 761 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8021 (tttp) REVERT: A 827 MET cc_start: 0.8134 (mmm) cc_final: 0.7813 (mmm) REVERT: A 848 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7597 (t) REVERT: A 872 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7389 (mp0) REVERT: A 875 THR cc_start: 0.7919 (p) cc_final: 0.7657 (p) REVERT: A 889 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7913 (tmm-80) REVERT: A 890 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7157 (mm-40) REVERT: A 893 MET cc_start: 0.8458 (mmm) cc_final: 0.8162 (mmm) REVERT: A 894 ASN cc_start: 0.8540 (m110) cc_final: 0.8196 (m110) REVERT: A 1090 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8055 (tppp) REVERT: A 1222 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7859 (mmmm) REVERT: A 1253 ASP cc_start: 0.7921 (t0) cc_final: 0.7591 (t0) REVERT: A 1263 ASN cc_start: 0.8169 (p0) cc_final: 0.7895 (p0) REVERT: A 1314 MET cc_start: 0.6612 (ttp) cc_final: 0.6231 (ttp) REVERT: A 1505 ASP cc_start: 0.7731 (t0) cc_final: 0.7519 (t0) REVERT: A 1511 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 1957 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7737 (t-100) REVERT: A 1959 LYS cc_start: 0.8444 (ttmm) cc_final: 0.8206 (ttmm) REVERT: A 2052 ASP cc_start: 0.8198 (t70) cc_final: 0.7908 (t70) REVERT: A 2072 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6233 (pt0) REVERT: A 2102 MET cc_start: 0.3266 (ppp) cc_final: 0.2845 (pp-130) REVERT: A 2176 MET cc_start: 0.6328 (tpt) cc_final: 0.6020 (tpt) REVERT: A 2211 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8099 (pp) REVERT: A 2219 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7809 (mp0) REVERT: A 2227 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6926 (tpp-160) REVERT: A 2520 LYS cc_start: 0.7684 (mttt) cc_final: 0.7322 (mttm) REVERT: A 2544 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 2616 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 2618 ILE cc_start: 0.8784 (mm) cc_final: 0.8514 (mp) REVERT: A 2630 ASN cc_start: 0.8318 (t0) cc_final: 0.7997 (t0) REVERT: A 2674 ASP cc_start: 0.8012 (m-30) cc_final: 0.7793 (m-30) REVERT: A 2685 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8780 (p) REVERT: A 2753 THR cc_start: 0.6795 (m) cc_final: 0.6326 (p) REVERT: B 27 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 28 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8392 (ttmm) REVERT: B 45 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: B 63 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7571 (mp0) REVERT: B 387 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8323 (ttmm) REVERT: B 501 GLN cc_start: 0.7940 (mt0) cc_final: 0.7630 (mt0) REVERT: B 505 MET cc_start: 0.7103 (mmm) cc_final: 0.6632 (mmm) REVERT: B 563 GLU cc_start: 0.7106 (pp20) cc_final: 0.6730 (pp20) REVERT: B 834 ASP cc_start: 0.7960 (p0) cc_final: 0.7625 (p0) REVERT: B 836 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8511 (mt) REVERT: B 885 TYR cc_start: 0.8534 (t80) cc_final: 0.8221 (t80) REVERT: B 889 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7618 (mtm-85) REVERT: B 1082 LYS cc_start: 0.7847 (pptt) cc_final: 0.7642 (pptt) REVERT: B 1090 LYS cc_start: 0.8647 (tppp) cc_final: 0.8152 (tppp) REVERT: B 1094 ASP cc_start: 0.7726 (m-30) cc_final: 0.7372 (m-30) REVERT: B 1143 GLU cc_start: 0.7338 (tp30) cc_final: 0.7018 (tp30) REVERT: B 1148 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 1511 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 1691 LEU cc_start: 0.0849 (OUTLIER) cc_final: -0.0591 (mt) REVERT: B 1821 TYR cc_start: 0.8348 (t80) cc_final: 0.7977 (t80) REVERT: B 1823 ASP cc_start: 0.7472 (m-30) cc_final: 0.7208 (m-30) REVERT: B 1833 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: B 1850 GLU cc_start: 0.7941 (tp30) cc_final: 0.7727 (tp30) REVERT: B 2074 LEU cc_start: 0.8219 (mp) cc_final: 0.7964 (mt) REVERT: B 2166 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8525 (tm) REVERT: B 2221 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8062 (mtmm) REVERT: B 2301 GLN cc_start: 0.8597 (tt0) cc_final: 0.8342 (mt0) REVERT: B 2562 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8331 (ttpp) REVERT: B 2563 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8553 (m) REVERT: B 2564 ASN cc_start: 0.8440 (p0) cc_final: 0.8181 (p0) REVERT: B 2565 TRP cc_start: 0.8154 (t60) cc_final: 0.7514 (t60) REVERT: B 2575 MET cc_start: 0.7269 (tpp) cc_final: 0.6947 (tpp) REVERT: B 2649 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: B 2674 ASP cc_start: 0.7959 (m-30) cc_final: 0.7437 (m-30) REVERT: B 2708 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6649 (mm) REVERT: B 2723 MET cc_start: 0.7524 (tpp) cc_final: 0.6708 (tpp) REVERT: B 2743 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8248 (mt-10) outliers start: 163 outliers final: 95 residues processed: 723 average time/residue: 1.3833 time to fit residues: 1166.1097 Evaluate side-chains 714 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 600 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1719 ARG Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1818 LYS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1957 TRP Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2057 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain A residue 2166 LEU Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2227 ARG Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2550 LEU Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2685 VAL Chi-restraints excluded: chain A residue 2746 PHE Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain A residue 2789 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 889 ARG Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1691 LEU Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1811 SER Chi-restraints excluded: chain B residue 1833 GLU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2166 LEU Chi-restraints excluded: chain B residue 2176 MET Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2548 ILE Chi-restraints excluded: chain B residue 2562 LYS Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2618 ILE Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2724 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 288 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 332 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 919 ASN A1411 ASN A1720 ASN A1962 ASN A2262 HIS A2542 GLN A2587 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 780 GLN B 782 ASN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1852 GLN ** B1929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS B1952 GLN B2093 ASN ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.159893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133418 restraints weight = 42756.674| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.49 r_work: 0.3715 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 27176 Z= 0.215 Angle : 0.660 10.961 36816 Z= 0.324 Chirality : 0.044 0.247 4144 Planarity : 0.005 0.081 4762 Dihedral : 5.743 55.665 3702 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.80 % Rotamer: Outliers : 5.04 % Allowed : 20.51 % Favored : 74.45 % 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: 0.51 (0.15), residues: 3326 helix: 1.41 (0.14), residues: 1452 sheet: 0.41 (0.30), residues: 304 loop : -0.67 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 765 HIS 0.007 0.001 HIS B 460 PHE 0.022 0.002 PHE A2040 TYR 0.025 0.002 TYR A2506 ARG 0.012 0.001 ARG B2233 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 1175) hydrogen bonds : angle 4.13066 ( 3387) metal coordination : bond 0.01241 ( 24) metal coordination : angle 3.01214 ( 28) covalent geometry : bond 0.00501 (27152) covalent geometry : angle 0.65531 (36788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 624 time to evaluate : 2.832 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 17 GLN cc_start: 0.7990 (mp10) cc_final: 0.7307 (mp10) REVERT: A 41 ASN cc_start: 0.8225 (t0) cc_final: 0.8013 (p0) REVERT: A 49 LYS cc_start: 0.8744 (tptt) cc_final: 0.8239 (mmmm) REVERT: A 57 HIS cc_start: 0.7259 (m-70) cc_final: 0.6933 (m-70) REVERT: A 75 GLN cc_start: 0.7986 (pm20) cc_final: 0.6752 (pp30) REVERT: A 361 GLN cc_start: 0.8192 (pt0) cc_final: 0.7920 (pt0) REVERT: A 392 GLN cc_start: 0.7812 (pp30) cc_final: 0.7041 (pt0) REVERT: A 426 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6932 (mm) REVERT: A 494 TRP cc_start: 0.7743 (p-90) cc_final: 0.7459 (p-90) REVERT: A 736 LYS cc_start: 0.8043 (ptmm) cc_final: 0.7447 (ptpp) REVERT: A 745 GLU cc_start: 0.8068 (mp0) cc_final: 0.7839 (mp0) REVERT: A 827 MET cc_start: 0.8200 (mmm) cc_final: 0.7880 (mmm) REVERT: A 867 ILE cc_start: 0.8625 (mm) cc_final: 0.8335 (mm) REVERT: A 872 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7409 (mp0) REVERT: A 875 THR cc_start: 0.7921 (p) cc_final: 0.7649 (p) REVERT: A 889 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7931 (tmm-80) REVERT: A 890 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7132 (mm-40) REVERT: A 893 MET cc_start: 0.8488 (mmm) cc_final: 0.8168 (mmm) REVERT: A 894 ASN cc_start: 0.8553 (m110) cc_final: 0.8216 (m110) REVERT: A 1090 LYS cc_start: 0.8363 (ttmm) cc_final: 0.7982 (tppp) REVERT: A 1222 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7789 (mmmm) REVERT: A 1239 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8340 (ttpp) REVERT: A 1263 ASN cc_start: 0.8214 (p0) cc_final: 0.7932 (p0) REVERT: A 1314 MET cc_start: 0.6635 (ttp) cc_final: 0.6254 (ttp) REVERT: A 1405 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8079 (mp) REVERT: A 1505 ASP cc_start: 0.7749 (t0) cc_final: 0.7528 (t0) REVERT: A 1511 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 1881 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4573 (mtt180) REVERT: A 1957 TRP cc_start: 0.8620 (OUTLIER) cc_final: 0.7702 (t-100) REVERT: A 1959 LYS cc_start: 0.8469 (ttmm) cc_final: 0.8185 (ttmm) REVERT: A 2052 ASP cc_start: 0.8266 (t70) cc_final: 0.7768 (t70) REVERT: A 2053 GLN cc_start: 0.8169 (mp10) cc_final: 0.7457 (mp10) REVERT: A 2072 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6112 (pt0) REVERT: A 2102 MET cc_start: 0.3371 (ppp) cc_final: 0.2882 (pp-130) REVERT: A 2178 MET cc_start: 0.7519 (pmm) cc_final: 0.7221 (pmt) REVERT: A 2211 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8118 (pp) REVERT: A 2227 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7013 (tpp-160) REVERT: A 2237 SER cc_start: 0.6846 (OUTLIER) cc_final: 0.5783 (m) REVERT: A 2520 LYS cc_start: 0.7764 (mttt) cc_final: 0.7466 (mttt) REVERT: A 2544 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7628 (mm-30) REVERT: A 2616 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 2618 ILE cc_start: 0.8805 (mm) cc_final: 0.8534 (mp) REVERT: A 2630 ASN cc_start: 0.8362 (t0) cc_final: 0.8003 (t0) REVERT: A 2685 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8788 (p) REVERT: A 2753 THR cc_start: 0.6797 (m) cc_final: 0.6280 (p) REVERT: B 27 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 28 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8433 (ttmm) REVERT: B 45 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: B 63 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7626 (mp0) REVERT: B 501 GLN cc_start: 0.8005 (mt0) cc_final: 0.7676 (mt0) REVERT: B 505 MET cc_start: 0.7144 (mmm) cc_final: 0.6660 (mmm) REVERT: B 563 GLU cc_start: 0.7161 (pp20) cc_final: 0.6851 (pp20) REVERT: B 834 ASP cc_start: 0.7987 (p0) cc_final: 0.7681 (p0) REVERT: B 872 GLU cc_start: 0.7875 (mp0) cc_final: 0.7643 (mp0) REVERT: B 885 TYR cc_start: 0.8671 (t80) cc_final: 0.8345 (t80) REVERT: B 889 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7745 (mtm-85) REVERT: B 1082 LYS cc_start: 0.7888 (pptt) cc_final: 0.7662 (pptt) REVERT: B 1090 LYS cc_start: 0.8678 (tppp) cc_final: 0.8260 (tppp) REVERT: B 1094 ASP cc_start: 0.7853 (m-30) cc_final: 0.7533 (m-30) REVERT: B 1143 GLU cc_start: 0.7389 (tp30) cc_final: 0.7048 (tp30) REVERT: B 1148 GLU cc_start: 0.8206 (mm-30) cc_final: 0.8004 (mm-30) REVERT: B 1366 GLU cc_start: 0.5967 (tp30) cc_final: 0.5738 (tp30) REVERT: B 1511 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7423 (tm-30) REVERT: B 1691 LEU cc_start: 0.0925 (OUTLIER) cc_final: -0.0529 (mt) REVERT: B 1823 ASP cc_start: 0.7565 (m-30) cc_final: 0.7311 (m-30) REVERT: B 1833 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 1850 GLU cc_start: 0.7965 (tp30) cc_final: 0.7741 (tp30) REVERT: B 2218 PHE cc_start: 0.8524 (t80) cc_final: 0.8209 (t80) REVERT: B 2225 PHE cc_start: 0.8540 (t80) cc_final: 0.8322 (t80) REVERT: B 2301 GLN cc_start: 0.8659 (tt0) cc_final: 0.8407 (mt0) REVERT: B 2562 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8310 (ttpp) REVERT: B 2563 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8555 (m) REVERT: B 2564 ASN cc_start: 0.8440 (p0) cc_final: 0.8194 (p0) REVERT: B 2575 MET cc_start: 0.7268 (tpp) cc_final: 0.6964 (tpp) REVERT: B 2598 MET cc_start: 0.7438 (ptp) cc_final: 0.7059 (ppp) REVERT: B 2674 ASP cc_start: 0.7930 (m-30) cc_final: 0.7673 (m-30) REVERT: B 2708 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6698 (mm) REVERT: B 2723 MET cc_start: 0.7579 (tpp) cc_final: 0.6810 (tpp) outliers start: 150 outliers final: 86 residues processed: 717 average time/residue: 1.7363 time to fit residues: 1463.7935 Evaluate side-chains 703 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 600 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1235 TRP Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1411 ASN Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1719 ARG Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1881 ARG Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1957 TRP Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain A residue 2166 LEU Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2227 ARG Chi-restraints excluded: chain A residue 2237 SER Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2550 LEU Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2685 VAL Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 889 ARG Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1691 LEU Chi-restraints excluded: chain B residue 1696 GLU Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1833 GLU Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2176 MET Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2548 ILE Chi-restraints excluded: chain B residue 2562 LYS Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2708 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 330 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 264 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 182 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 ASN A1962 ASN A2262 HIS A2527 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2587 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 GLN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1929 ASN B1932 HIS ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.160685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.134326 restraints weight = 42756.645| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.50 r_work: 0.3739 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27176 Z= 0.138 Angle : 0.642 10.358 36816 Z= 0.313 Chirality : 0.041 0.234 4144 Planarity : 0.005 0.060 4762 Dihedral : 5.613 55.615 3697 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.46 % Rotamer: Outliers : 4.47 % Allowed : 21.72 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3326 helix: 1.49 (0.14), residues: 1456 sheet: 0.45 (0.30), residues: 304 loop : -0.64 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 765 HIS 0.013 0.001 HIS B 460 PHE 0.020 0.001 PHE A2040 TYR 0.028 0.001 TYR B 401 ARG 0.013 0.000 ARG B2233 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 1175) hydrogen bonds : angle 4.05640 ( 3387) metal coordination : bond 0.00713 ( 24) metal coordination : angle 2.64845 ( 28) covalent geometry : bond 0.00324 (27152) covalent geometry : angle 0.63824 (36788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 625 time to evaluate : 3.510 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 17 GLN cc_start: 0.7954 (mp10) cc_final: 0.7226 (mp10) REVERT: A 41 ASN cc_start: 0.8193 (t0) cc_final: 0.7980 (p0) REVERT: A 49 LYS cc_start: 0.8745 (tptt) cc_final: 0.8250 (mmmm) REVERT: A 57 HIS cc_start: 0.7227 (m-70) cc_final: 0.6904 (m-70) REVERT: A 75 GLN cc_start: 0.7957 (pm20) cc_final: 0.6779 (pp30) REVERT: A 361 GLN cc_start: 0.8155 (pt0) cc_final: 0.7859 (pt0) REVERT: A 426 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6895 (mm) REVERT: A 736 LYS cc_start: 0.8048 (ptmm) cc_final: 0.7458 (ptpp) REVERT: A 745 GLU cc_start: 0.8057 (mp0) cc_final: 0.7775 (mp0) REVERT: A 827 MET cc_start: 0.8183 (mmm) cc_final: 0.7854 (mmm) REVERT: A 867 ILE cc_start: 0.8609 (mm) cc_final: 0.8329 (mm) REVERT: A 872 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7399 (mp0) REVERT: A 875 THR cc_start: 0.7922 (p) cc_final: 0.7665 (p) REVERT: A 889 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7909 (tmm-80) REVERT: A 890 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7143 (mm-40) REVERT: A 893 MET cc_start: 0.8465 (mmm) cc_final: 0.8130 (mmm) REVERT: A 894 ASN cc_start: 0.8559 (m110) cc_final: 0.8191 (m110) REVERT: A 1090 LYS cc_start: 0.8327 (ttmm) cc_final: 0.7934 (tppp) REVERT: A 1222 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7905 (mmmm) REVERT: A 1239 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8327 (ttpp) REVERT: A 1263 ASN cc_start: 0.8196 (p0) cc_final: 0.7904 (p0) REVERT: A 1314 MET cc_start: 0.6576 (ttp) cc_final: 0.6213 (ttp) REVERT: A 1505 ASP cc_start: 0.7730 (t0) cc_final: 0.7494 (t0) REVERT: A 1511 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7303 (tm-30) REVERT: A 1833 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: A 1881 ARG cc_start: 0.4699 (OUTLIER) cc_final: 0.3949 (mpp-170) REVERT: A 1957 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.7732 (t-100) REVERT: A 1959 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8170 (ttmm) REVERT: A 2052 ASP cc_start: 0.8214 (t70) cc_final: 0.7916 (t70) REVERT: A 2072 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.5991 (pt0) REVERT: A 2102 MET cc_start: 0.3264 (ppp) cc_final: 0.2865 (pp-130) REVERT: A 2176 MET cc_start: 0.6537 (tpt) cc_final: 0.6276 (tpp) REVERT: A 2211 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8101 (pp) REVERT: A 2227 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7048 (tpp-160) REVERT: A 2520 LYS cc_start: 0.7689 (mttt) cc_final: 0.7259 (mttp) REVERT: A 2544 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 2616 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7588 (mt-10) REVERT: A 2630 ASN cc_start: 0.8369 (t0) cc_final: 0.8032 (t0) REVERT: A 2717 ILE cc_start: 0.8323 (pp) cc_final: 0.8015 (pt) REVERT: A 2753 THR cc_start: 0.6748 (m) cc_final: 0.6261 (p) REVERT: B 27 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 28 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8448 (ttmm) REVERT: B 45 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: B 63 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7615 (mp0) REVERT: B 501 GLN cc_start: 0.7944 (mt0) cc_final: 0.7629 (mt0) REVERT: B 505 MET cc_start: 0.7062 (mmm) cc_final: 0.6599 (mmm) REVERT: B 563 GLU cc_start: 0.7116 (pp20) cc_final: 0.6725 (pp20) REVERT: B 745 GLU cc_start: 0.7642 (mp0) cc_final: 0.7441 (mp0) REVERT: B 834 ASP cc_start: 0.7963 (p0) cc_final: 0.7589 (p0) REVERT: B 848 VAL cc_start: 0.8709 (p) cc_final: 0.8436 (m) REVERT: B 872 GLU cc_start: 0.7871 (mp0) cc_final: 0.7629 (mp0) REVERT: B 885 TYR cc_start: 0.8616 (t80) cc_final: 0.8313 (t80) REVERT: B 886 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 889 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7718 (mtm-85) REVERT: B 1082 LYS cc_start: 0.7845 (pptt) cc_final: 0.7627 (pptt) REVERT: B 1090 LYS cc_start: 0.8652 (tppp) cc_final: 0.8213 (tppp) REVERT: B 1094 ASP cc_start: 0.7746 (m-30) cc_final: 0.7418 (m-30) REVERT: B 1143 GLU cc_start: 0.7348 (tp30) cc_final: 0.7009 (tp30) REVERT: B 1148 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 1263 ASN cc_start: 0.8203 (p0) cc_final: 0.7922 (p0) REVERT: B 1511 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 1691 LEU cc_start: 0.0961 (OUTLIER) cc_final: -0.0482 (mt) REVERT: B 1823 ASP cc_start: 0.7583 (m-30) cc_final: 0.7315 (m-30) REVERT: B 1833 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: B 2086 MET cc_start: 0.7192 (ptm) cc_final: 0.6902 (ptt) REVERT: B 2301 GLN cc_start: 0.8610 (tt0) cc_final: 0.8324 (mt0) REVERT: B 2540 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7961 (mm) REVERT: B 2562 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8343 (ttpp) REVERT: B 2563 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8593 (m) REVERT: B 2564 ASN cc_start: 0.8449 (p0) cc_final: 0.8216 (p0) REVERT: B 2565 TRP cc_start: 0.8171 (t60) cc_final: 0.7529 (t60) REVERT: B 2575 MET cc_start: 0.7280 (tpp) cc_final: 0.6963 (tpp) REVERT: B 2598 MET cc_start: 0.7388 (ptp) cc_final: 0.7000 (ppp) REVERT: B 2708 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6698 (mm) REVERT: B 2723 MET cc_start: 0.7593 (tpp) cc_final: 0.6788 (tpp) outliers start: 133 outliers final: 89 residues processed: 705 average time/residue: 1.6797 time to fit residues: 1389.8910 Evaluate side-chains 719 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 614 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1235 TRP Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1719 ARG Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1818 LYS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1881 ARG Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1957 TRP Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2072 GLN Chi-restraints excluded: chain A residue 2086 MET Chi-restraints excluded: chain A residue 2166 LEU Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2227 ARG Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2550 LEU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2724 THR Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 889 ARG Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1691 LEU Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1833 GLU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2176 MET Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2548 ILE Chi-restraints excluded: chain B residue 2562 LYS Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2618 ILE Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2708 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 194 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 237 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 269 optimal weight: 0.0050 chunk 250 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 321 optimal weight: 0.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1411 ASN A1720 ASN A1962 ASN A2262 HIS ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2587 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS B1952 GLN ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.161176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134864 restraints weight = 42774.692| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.49 r_work: 0.3735 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27176 Z= 0.153 Angle : 0.659 11.028 36816 Z= 0.322 Chirality : 0.042 0.254 4144 Planarity : 0.005 0.061 4762 Dihedral : 5.588 55.498 3693 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % Rotamer: Outliers : 4.24 % Allowed : 22.29 % Favored : 73.47 % 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: 0.58 (0.15), residues: 3326 helix: 1.50 (0.14), residues: 1446 sheet: 0.43 (0.30), residues: 304 loop : -0.66 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP A 765 HIS 0.015 0.001 HIS B 460 PHE 0.031 0.001 PHE B2675 TYR 0.026 0.002 TYR A2506 ARG 0.013 0.001 ARG B2233 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1175) hydrogen bonds : angle 4.07762 ( 3387) metal coordination : bond 0.00824 ( 24) metal coordination : angle 2.66064 ( 28) covalent geometry : bond 0.00364 (27152) covalent geometry : angle 0.65525 (36788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 620 time to evaluate : 3.301 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 17 GLN cc_start: 0.7982 (mp10) cc_final: 0.7274 (mp10) REVERT: A 41 ASN cc_start: 0.8211 (t0) cc_final: 0.7988 (p0) REVERT: A 49 LYS cc_start: 0.8748 (tptt) cc_final: 0.8259 (mmmm) REVERT: A 57 HIS cc_start: 0.7233 (m-70) cc_final: 0.6906 (m-70) REVERT: A 75 GLN cc_start: 0.7950 (pm20) cc_final: 0.6770 (pp30) REVERT: A 361 GLN cc_start: 0.8147 (pt0) cc_final: 0.7850 (pt0) REVERT: A 426 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6935 (mm) REVERT: A 736 LYS cc_start: 0.8065 (ptmm) cc_final: 0.7491 (ptpp) REVERT: A 745 GLU cc_start: 0.8062 (mp0) cc_final: 0.7757 (mp0) REVERT: A 765 TRP cc_start: 0.7641 (t60) cc_final: 0.7317 (t60) REVERT: A 827 MET cc_start: 0.8200 (mmm) cc_final: 0.7880 (mmm) REVERT: A 867 ILE cc_start: 0.8620 (mm) cc_final: 0.8354 (mm) REVERT: A 872 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7425 (mp0) REVERT: A 875 THR cc_start: 0.7923 (p) cc_final: 0.7676 (p) REVERT: A 889 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7930 (tmm-80) REVERT: A 890 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7181 (mm-40) REVERT: A 893 MET cc_start: 0.8473 (mmm) cc_final: 0.8149 (mmm) REVERT: A 894 ASN cc_start: 0.8558 (m110) cc_final: 0.8192 (m110) REVERT: A 1090 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7913 (tppp) REVERT: A 1139 ILE cc_start: 0.8599 (mt) cc_final: 0.8348 (mp) REVERT: A 1222 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7857 (mmmm) REVERT: A 1239 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8355 (ttpp) REVERT: A 1263 ASN cc_start: 0.8161 (p0) cc_final: 0.7868 (p0) REVERT: A 1314 MET cc_start: 0.6580 (ttp) cc_final: 0.6223 (ttp) REVERT: A 1505 ASP cc_start: 0.7726 (t0) cc_final: 0.7491 (t0) REVERT: A 1511 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 1833 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: A 1881 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4658 (mtt180) REVERT: A 1957 TRP cc_start: 0.8596 (OUTLIER) cc_final: 0.7687 (t-100) REVERT: A 1959 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8175 (ttmm) REVERT: A 2052 ASP cc_start: 0.8203 (t70) cc_final: 0.7910 (t70) REVERT: A 2102 MET cc_start: 0.3332 (ppp) cc_final: 0.2936 (pp-130) REVERT: A 2178 MET cc_start: 0.7378 (pmm) cc_final: 0.7126 (pmt) REVERT: A 2211 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8104 (pp) REVERT: A 2227 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7072 (tpp-160) REVERT: A 2237 SER cc_start: 0.6777 (OUTLIER) cc_final: 0.5725 (m) REVERT: A 2520 LYS cc_start: 0.7674 (mttt) cc_final: 0.7351 (mttt) REVERT: A 2544 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7652 (mm-30) REVERT: A 2616 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 2630 ASN cc_start: 0.8395 (t0) cc_final: 0.8032 (t0) REVERT: B 27 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7705 (tm-30) REVERT: B 28 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8444 (ttmm) REVERT: B 45 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: B 63 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7629 (mp0) REVERT: B 501 GLN cc_start: 0.7968 (mt0) cc_final: 0.7653 (mt0) REVERT: B 505 MET cc_start: 0.7063 (mmm) cc_final: 0.6601 (mmm) REVERT: B 507 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 563 GLU cc_start: 0.7125 (pp20) cc_final: 0.6765 (pp20) REVERT: B 834 ASP cc_start: 0.7989 (p0) cc_final: 0.7614 (p0) REVERT: B 848 VAL cc_start: 0.8746 (p) cc_final: 0.8477 (m) REVERT: B 872 GLU cc_start: 0.7883 (mp0) cc_final: 0.7642 (mp0) REVERT: B 885 TYR cc_start: 0.8635 (t80) cc_final: 0.8387 (t80) REVERT: B 1082 LYS cc_start: 0.7851 (pptt) cc_final: 0.7637 (pptt) REVERT: B 1090 LYS cc_start: 0.8670 (tppp) cc_final: 0.8238 (tppp) REVERT: B 1094 ASP cc_start: 0.7745 (m-30) cc_final: 0.7407 (m-30) REVERT: B 1143 GLU cc_start: 0.7361 (tp30) cc_final: 0.7025 (tp30) REVERT: B 1148 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7965 (mm-30) REVERT: B 1263 ASN cc_start: 0.8218 (p0) cc_final: 0.7934 (p0) REVERT: B 1511 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 1691 LEU cc_start: 0.0908 (OUTLIER) cc_final: -0.0543 (mt) REVERT: B 1823 ASP cc_start: 0.7583 (m-30) cc_final: 0.7313 (m-30) REVERT: B 1833 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: B 2301 GLN cc_start: 0.8609 (tt0) cc_final: 0.8323 (mt0) REVERT: B 2540 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7982 (mm) REVERT: B 2562 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8347 (ttpp) REVERT: B 2563 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8594 (m) REVERT: B 2564 ASN cc_start: 0.8455 (p0) cc_final: 0.8231 (p0) REVERT: B 2565 TRP cc_start: 0.8183 (t60) cc_final: 0.7532 (t60) REVERT: B 2575 MET cc_start: 0.7303 (tpp) cc_final: 0.6974 (tpp) REVERT: B 2598 MET cc_start: 0.7416 (ptp) cc_final: 0.7056 (ppp) REVERT: B 2637 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7569 (mmmm) REVERT: B 2708 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6706 (mm) REVERT: B 2723 MET cc_start: 0.7600 (tpp) cc_final: 0.6805 (tpp) outliers start: 126 outliers final: 84 residues processed: 699 average time/residue: 1.4035 time to fit residues: 1149.3022 Evaluate side-chains 704 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 605 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1235 TRP Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1818 LYS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1881 ARG Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1957 TRP Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2086 MET Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2227 ARG Chi-restraints excluded: chain A residue 2237 SER Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2550 LEU Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2724 THR Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1691 LEU Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1833 GLU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2176 MET Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 LEU Chi-restraints excluded: chain B residue 2548 ILE Chi-restraints excluded: chain B residue 2558 LEU Chi-restraints excluded: chain B residue 2562 LYS Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2618 ILE Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2708 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 227 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 209 optimal weight: 0.6980 chunk 328 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1411 ASN A1962 ASN A2236 GLN A2262 HIS ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2587 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1929 ASN B1932 HIS B1952 GLN ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.161112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.134955 restraints weight = 42704.292| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.49 r_work: 0.3741 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27176 Z= 0.143 Angle : 0.672 13.126 36816 Z= 0.326 Chirality : 0.042 0.250 4144 Planarity : 0.005 0.060 4762 Dihedral : 5.560 55.442 3693 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 3.73 % Allowed : 22.93 % Favored : 73.34 % 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: 0.59 (0.15), residues: 3326 helix: 1.51 (0.14), residues: 1446 sheet: 0.42 (0.30), residues: 294 loop : -0.64 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP A 765 HIS 0.015 0.001 HIS B 460 PHE 0.021 0.001 PHE A2040 TYR 0.019 0.001 TYR B 401 ARG 0.012 0.000 ARG B2233 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 1175) hydrogen bonds : angle 4.06811 ( 3387) metal coordination : bond 0.00708 ( 24) metal coordination : angle 2.61600 ( 28) covalent geometry : bond 0.00340 (27152) covalent geometry : angle 0.66822 (36788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 617 time to evaluate : 3.031 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 17 GLN cc_start: 0.7949 (mp10) cc_final: 0.7268 (mp10) REVERT: A 41 ASN cc_start: 0.8231 (t0) cc_final: 0.8004 (p0) REVERT: A 49 LYS cc_start: 0.8750 (tptt) cc_final: 0.8265 (mmmm) REVERT: A 57 HIS cc_start: 0.7193 (m-70) cc_final: 0.6887 (m-70) REVERT: A 75 GLN cc_start: 0.7959 (pm20) cc_final: 0.6804 (pp30) REVERT: A 361 GLN cc_start: 0.8104 (pt0) cc_final: 0.7800 (pt0) REVERT: A 426 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6927 (mm) REVERT: A 736 LYS cc_start: 0.8039 (ptmm) cc_final: 0.7484 (ptpp) REVERT: A 745 GLU cc_start: 0.8106 (mp0) cc_final: 0.7808 (mp0) REVERT: A 765 TRP cc_start: 0.7594 (t60) cc_final: 0.7135 (t60) REVERT: A 827 MET cc_start: 0.8156 (mmm) cc_final: 0.7846 (mmm) REVERT: A 867 ILE cc_start: 0.8624 (mm) cc_final: 0.8383 (mm) REVERT: A 872 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7424 (mp0) REVERT: A 875 THR cc_start: 0.7892 (p) cc_final: 0.7649 (p) REVERT: A 889 ARG cc_start: 0.8605 (tmm-80) cc_final: 0.8074 (tmm-80) REVERT: A 893 MET cc_start: 0.8456 (mmm) cc_final: 0.8179 (mmm) REVERT: A 894 ASN cc_start: 0.8572 (m110) cc_final: 0.8203 (m110) REVERT: A 1090 LYS cc_start: 0.8330 (ttmm) cc_final: 0.7934 (tppp) REVERT: A 1239 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8338 (ttpp) REVERT: A 1263 ASN cc_start: 0.8170 (p0) cc_final: 0.7875 (p0) REVERT: A 1314 MET cc_start: 0.6557 (ttp) cc_final: 0.6209 (ttp) REVERT: A 1505 ASP cc_start: 0.7721 (t0) cc_final: 0.7504 (t0) REVERT: A 1511 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 1833 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 1881 ARG cc_start: 0.5087 (OUTLIER) cc_final: 0.4503 (mpp-170) REVERT: A 1957 TRP cc_start: 0.8630 (OUTLIER) cc_final: 0.7645 (t-100) REVERT: A 1959 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8181 (ttmm) REVERT: A 2052 ASP cc_start: 0.8207 (t70) cc_final: 0.7900 (t70) REVERT: A 2102 MET cc_start: 0.3343 (ppp) cc_final: 0.2945 (pp-130) REVERT: A 2211 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8096 (pp) REVERT: A 2227 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7090 (tpp-160) REVERT: A 2520 LYS cc_start: 0.7634 (mttt) cc_final: 0.7262 (mttm) REVERT: A 2544 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 2616 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7570 (mt-10) REVERT: A 2630 ASN cc_start: 0.8377 (t0) cc_final: 0.8011 (t0) REVERT: B 27 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 28 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8405 (ttmm) REVERT: B 45 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: B 63 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7636 (mp0) REVERT: B 501 GLN cc_start: 0.7917 (mt0) cc_final: 0.7618 (mt0) REVERT: B 505 MET cc_start: 0.7019 (mmm) cc_final: 0.6595 (mmm) REVERT: B 507 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 563 GLU cc_start: 0.7205 (pp20) cc_final: 0.6867 (pp20) REVERT: B 834 ASP cc_start: 0.7961 (p0) cc_final: 0.7646 (p0) REVERT: B 848 VAL cc_start: 0.8765 (p) cc_final: 0.8493 (m) REVERT: B 885 TYR cc_start: 0.8627 (t80) cc_final: 0.8409 (t80) REVERT: B 1082 LYS cc_start: 0.7855 (pptt) cc_final: 0.7636 (pptt) REVERT: B 1090 LYS cc_start: 0.8658 (tppp) cc_final: 0.8221 (tppp) REVERT: B 1094 ASP cc_start: 0.7680 (m-30) cc_final: 0.7391 (m-30) REVERT: B 1143 GLU cc_start: 0.7340 (tp30) cc_final: 0.7026 (tp30) REVERT: B 1148 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7986 (mm-30) REVERT: B 1511 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 1691 LEU cc_start: 0.0810 (OUTLIER) cc_final: -0.0600 (mt) REVERT: B 1823 ASP cc_start: 0.7547 (m-30) cc_final: 0.7273 (m-30) REVERT: B 1833 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: B 2301 GLN cc_start: 0.8599 (tt0) cc_final: 0.8341 (mt0) REVERT: B 2562 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8341 (ttpp) REVERT: B 2563 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8605 (m) REVERT: B 2564 ASN cc_start: 0.8445 (p0) cc_final: 0.8218 (p0) REVERT: B 2565 TRP cc_start: 0.8173 (t60) cc_final: 0.7519 (t60) REVERT: B 2575 MET cc_start: 0.7288 (tpp) cc_final: 0.6966 (tpp) REVERT: B 2598 MET cc_start: 0.7401 (ptp) cc_final: 0.7052 (ppp) REVERT: B 2637 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7597 (mmmm) REVERT: B 2708 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6668 (mm) REVERT: B 2723 MET cc_start: 0.7606 (tpp) cc_final: 0.6828 (tpp) outliers start: 111 outliers final: 87 residues processed: 688 average time/residue: 1.3692 time to fit residues: 1105.9998 Evaluate side-chains 705 residues out of total 2974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 606 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1225 ARG Chi-restraints excluded: chain A residue 1231 TYR Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1411 ASN Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1697 ARG Chi-restraints excluded: chain A residue 1698 THR Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1818 LYS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1881 ARG Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1957 TRP Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2086 MET Chi-restraints excluded: chain A residue 2175 PHE Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2227 ARG Chi-restraints excluded: chain A residue 2240 LEU Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2550 LEU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2724 THR Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1241 LYS Chi-restraints excluded: chain B residue 1298 ILE Chi-restraints excluded: chain B residue 1443 MET Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1691 LEU Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1833 GLU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1881 ARG Chi-restraints excluded: chain B residue 1924 LEU Chi-restraints excluded: chain B residue 1935 VAL Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2176 MET Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2548 ILE Chi-restraints excluded: chain B residue 2562 LYS Chi-restraints excluded: chain B residue 2563 VAL Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2618 ILE Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2708 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 10 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 161 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 127 optimal weight: 0.0980 chunk 285 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1411 ASN A1720 ASN A1962 ASN A2542 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS B1952 GLN ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.160836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134508 restraints weight = 43052.553| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.50 r_work: 0.3742 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27176 Z= 0.143 Angle : 0.680 12.645 36816 Z= 0.329 Chirality : 0.042 0.261 4144 Planarity : 0.005 0.070 4762 Dihedral : 5.421 55.322 3687 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 3.63 % Allowed : 23.40 % Favored : 72.97 % 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: 0.59 (0.15), residues: 3326 helix: 1.51 (0.14), residues: 1446 sheet: 0.43 (0.30), residues: 294 loop : -0.64 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP A 765 HIS 0.012 0.001 HIS B 460 PHE 0.031 0.001 PHE B2675 TYR 0.027 0.001 TYR A2506 ARG 0.016 0.000 ARG A2676 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 1175) hydrogen bonds : angle 4.06789 ( 3387) metal coordination : bond 0.00717 ( 24) metal coordination : angle 2.64720 ( 28) covalent geometry : bond 0.00341 (27152) covalent geometry : angle 0.67632 (36788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35663.59 seconds wall clock time: 620 minutes 49.60 seconds (37249.60 seconds total)