Starting phenix.real_space_refine on Wed Mar 20 06:24:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e0q_27822/03_2024/8e0q_27822.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e0q_27822/03_2024/8e0q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e0q_27822/03_2024/8e0q_27822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e0q_27822/03_2024/8e0q_27822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e0q_27822/03_2024/8e0q_27822.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e0q_27822/03_2024/8e0q_27822.pdb" } 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 Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2777": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.19, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.16 Conformation dependent library (CDL) restraints added in 5.1 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: 3.12 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: 11.93 Time building geometry restraints manager: 11.11 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: 99.20 - 106.16: 911 106.16 - 113.12: 14827 113.12 - 120.08: 9219 120.08 - 127.05: 11471 127.05 - 134.01: 360 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 2.440 nonbonded pdb=" O ASN B1962 " pdb=" OG1 THR B1965 " model vdw 2.222 2.440 nonbonded pdb=" O LYS A 370 " pdb=" OG SER A 386 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR B 14 " pdb=" OE1 GLN B 17 " model vdw 2.238 2.440 nonbonded pdb=" O LYS B 370 " pdb=" OG SER B 386 " model vdw 2.244 2.440 ... (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 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.350 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 75.690 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.110 ------------------------------------------------------------------------------- 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 27152 Z= 0.234 Angle : 0.542 10.385 36788 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 *********************** 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 fitting. rotamer outliers: 141 poor density : 728 time to evaluate : 2.789 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: 1.2812 time to fit residues: 1234.4905 Evaluate side-chains 698 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 624 time to evaluate : 2.565 ------------------------------------------------------------------------------- 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: 2.9990 chunk 86 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 263 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 924 HIS ** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 GLN A1411 ASN A1508 GLN A1720 ASN A1852 GLN ** A2072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2253 GLN A2260 ASN A2262 HIS A2275 HIS A2531 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2543 ASN A2587 GLN B 421 ASN B 441 ASN B 469 GLN B 780 GLN B 782 ASN B 794 GLN B 806 GLN B 849 HIS ** B 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2527 ASN B2614 GLN B2680 ASN B2727 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27152 Z= 0.306 Angle : 0.602 11.071 36788 Z= 0.301 Chirality : 0.042 0.193 4144 Planarity : 0.005 0.067 4762 Dihedral : 7.290 83.931 3779 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.17 % Rotamer: Outliers : 5.78 % Allowed : 15.77 % Favored : 78.45 % 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: 0.46 (0.15), residues: 3326 helix: 1.36 (0.14), residues: 1428 sheet: 0.27 (0.29), residues: 340 loop : -0.66 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1235 HIS 0.008 0.001 HIS B 460 PHE 0.022 0.002 PHE A1087 TYR 0.023 0.002 TYR A1370 ARG 0.010 0.001 ARG B1854 *********************** 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 818 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 646 time to evaluate : 3.168 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: 0.7628 (mp10) cc_final: 0.7024 (mp10) REVERT: A 49 LYS cc_start: 0.8633 (tptt) cc_final: 0.8080 (tppp) REVERT: A 75 GLN cc_start: 0.8019 (pm20) cc_final: 0.6605 (pp30) REVERT: A 361 GLN cc_start: 0.8219 (pt0) cc_final: 0.7985 (pt0) REVERT: A 426 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6943 (mm) REVERT: A 494 TRP cc_start: 0.7727 (p-90) cc_final: 0.7476 (p-90) REVERT: A 736 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7494 (ptpp) REVERT: A 765 TRP cc_start: 0.7354 (t60) cc_final: 0.7116 (t60) REVERT: A 822 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8511 (tpp) REVERT: A 848 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7664 (t) REVERT: A 875 THR cc_start: 0.7977 (p) cc_final: 0.7691 (p) REVERT: A 889 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7850 (tmm-80) REVERT: A 890 GLN cc_start: 0.8145 (mm-40) cc_final: 0.6950 (mm-40) REVERT: A 893 MET cc_start: 0.8077 (mmm) cc_final: 0.7863 (mmm) REVERT: A 894 ASN cc_start: 0.8506 (m110) cc_final: 0.8192 (m110) REVERT: A 1090 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7917 (tppp) REVERT: A 1195 GLU cc_start: 0.7253 (pm20) cc_final: 0.7049 (pm20) REVERT: A 1222 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7563 (mtmm) REVERT: A 1233 ASP cc_start: 0.7726 (p0) cc_final: 0.7389 (p0) REVERT: A 1235 TRP cc_start: 0.7961 (p-90) cc_final: 0.7745 (p-90) REVERT: A 1263 ASN cc_start: 0.7855 (p0) cc_final: 0.7633 (p0) REVERT: A 1314 MET cc_start: 0.6573 (ttp) cc_final: 0.6240 (ttp) REVERT: A 1505 ASP cc_start: 0.7782 (t0) cc_final: 0.7560 (t0) REVERT: A 1511 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7035 (tm-30) REVERT: A 1515 SER cc_start: 0.8057 (p) cc_final: 0.7764 (p) REVERT: A 1957 TRP cc_start: 0.8542 (t-100) cc_final: 0.8286 (t-100) REVERT: A 2024 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8161 (mtm110) REVERT: A 2030 THR cc_start: 0.8095 (t) cc_final: 0.7854 (p) REVERT: A 2052 ASP cc_start: 0.7817 (t70) cc_final: 0.7427 (t70) REVERT: A 2072 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.5879 (pt0) REVERT: A 2086 MET cc_start: 0.1522 (ptp) cc_final: -0.0875 (ptp) REVERT: A 2102 MET cc_start: 0.3095 (ppp) cc_final: 0.2723 (pp-130) REVERT: A 2176 MET cc_start: 0.5924 (tpt) cc_final: 0.5685 (tpt) REVERT: A 2178 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7176 (pmm) REVERT: A 2211 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8000 (pp) REVERT: A 2219 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7531 (mp0) REVERT: A 2237 SER cc_start: 0.6892 (OUTLIER) cc_final: 0.5801 (t) REVERT: A 2520 LYS cc_start: 0.7745 (mttt) cc_final: 0.7385 (mptt) REVERT: A 2544 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7460 (mm-30) REVERT: A 2630 ASN cc_start: 0.8267 (t0) cc_final: 0.8050 (t0) REVERT: A 2633 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7177 (tm-30) REVERT: A 2637 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7856 (mtpp) REVERT: A 2640 GLU cc_start: 0.7497 (mp0) cc_final: 0.7154 (mp0) REVERT: A 2674 ASP cc_start: 0.7743 (m-30) cc_final: 0.7508 (m-30) REVERT: A 2685 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8748 (p) REVERT: A 2689 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7201 (tpp) REVERT: A 2753 THR cc_start: 0.6745 (m) cc_final: 0.6426 (m) REVERT: A 2760 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: B 28 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8295 (ttmm) REVERT: B 44 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6994 (mm-30) REVERT: B 501 GLN cc_start: 0.7853 (mt0) cc_final: 0.7495 (mt0) REVERT: B 505 MET cc_start: 0.6806 (mmm) cc_final: 0.6360 (mmm) REVERT: B 573 ARG cc_start: 0.7321 (mtp85) cc_final: 0.7089 (mtp85) REVERT: B 655 GLU cc_start: 0.7731 (mp0) cc_final: 0.7502 (mp0) REVERT: B 834 ASP cc_start: 0.7556 (p0) cc_final: 0.7139 (p0) REVERT: B 884 ASP cc_start: 0.7904 (m-30) cc_final: 0.7480 (t0) REVERT: B 1082 LYS cc_start: 0.7801 (pptt) cc_final: 0.7481 (pptt) REVERT: B 1148 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7469 (mm-30) REVERT: B 1331 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7548 (mmm160) REVERT: B 1366 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5029 (tp30) REVERT: B 1511 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7224 (tp30) REVERT: B 1833 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: B 1931 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7632 (mt-10) REVERT: B 2026 SER cc_start: 0.8025 (p) cc_final: 0.7786 (t) REVERT: B 2083 LYS cc_start: 0.7648 (mptm) cc_final: 0.7402 (mmtm) REVERT: B 2166 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8572 (tm) REVERT: B 2248 ARG cc_start: 0.7109 (mpp-170) cc_final: 0.6906 (mpp-170) REVERT: B 2301 GLN cc_start: 0.8497 (tt0) cc_final: 0.8219 (mt0) REVERT: B 2562 LYS cc_start: 0.8417 (tmmm) cc_final: 0.8211 (ttpp) REVERT: B 2563 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8578 (m) REVERT: B 2565 TRP cc_start: 0.8210 (t60) cc_final: 0.7639 (t60) REVERT: B 2598 MET cc_start: 0.7289 (ptp) cc_final: 0.7061 (ptp) REVERT: B 2649 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7282 (pt0) REVERT: B 2674 ASP cc_start: 0.7689 (m-30) cc_final: 0.7358 (m-30) REVERT: B 2708 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6673 (mm) REVERT: B 2723 MET cc_start: 0.7239 (tpp) cc_final: 0.6565 (tpp) REVERT: B 2743 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7715 (mt-10) outliers start: 172 outliers final: 85 residues processed: 752 average time/residue: 1.2889 time to fit residues: 1133.4261 Evaluate side-chains 713 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 609 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR 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 426 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 VAL 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 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 1833 GLU Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2024 ARG 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 2539 CYS Chi-restraints excluded: chain A residue 2545 LEU Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2623 ASN Chi-restraints excluded: chain A residue 2651 LEU Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2661 VAL 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 2717 ILE Chi-restraints excluded: chain A residue 2760 GLN 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 43 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 500 SER 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 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 1164 ASN 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 1316 ASP Chi-restraints excluded: chain B residue 1331 ARG Chi-restraints excluded: chain B residue 1366 GLU Chi-restraints excluded: chain B residue 1690 MET Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1718 VAL Chi-restraints excluded: chain B residue 1833 GLU 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 1952 GLN 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 2306 ASN 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 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 2722 SER 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 169 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 305 optimal weight: 2.9990 chunk 330 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 303 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 GLN A1411 ASN A1720 ASN A1962 ASN ** A2072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2531 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 ASN B 794 GLN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS B1952 GLN ** B2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27152 Z= 0.234 Angle : 0.581 10.974 36788 Z= 0.289 Chirality : 0.041 0.190 4144 Planarity : 0.005 0.063 4762 Dihedral : 6.697 82.784 3745 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 6.09 % Allowed : 17.01 % Favored : 76.90 % 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: 0.50 (0.15), residues: 3326 helix: 1.43 (0.14), residues: 1428 sheet: 0.52 (0.30), residues: 304 loop : -0.70 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1235 HIS 0.006 0.001 HIS B1946 PHE 0.032 0.002 PHE A1087 TYR 0.027 0.002 TYR B 401 ARG 0.008 0.000 ARG A2755 *********************** 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 813 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 632 time to evaluate : 3.075 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: 0.7620 (mp10) cc_final: 0.7008 (mp10) REVERT: A 49 LYS cc_start: 0.8631 (tptt) cc_final: 0.8085 (tppp) REVERT: A 75 GLN cc_start: 0.7984 (pm20) cc_final: 0.6589 (pp30) REVERT: A 361 GLN cc_start: 0.8179 (pt0) cc_final: 0.7916 (pt0) REVERT: A 426 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6938 (mm) REVERT: A 433 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.5564 (ttt90) REVERT: A 494 TRP cc_start: 0.7690 (p-90) cc_final: 0.7232 (p-90) REVERT: A 822 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8513 (tpp) REVERT: A 848 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7673 (t) REVERT: A 872 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7095 (mp0) REVERT: A 875 THR cc_start: 0.7984 (p) cc_final: 0.7675 (p) REVERT: A 889 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7828 (tmm-80) REVERT: A 890 GLN cc_start: 0.8123 (mm-40) cc_final: 0.6957 (mm-40) REVERT: A 894 ASN cc_start: 0.8493 (m110) cc_final: 0.8175 (m110) REVERT: A 1090 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7909 (tppp) REVERT: A 1233 ASP cc_start: 0.7727 (p0) cc_final: 0.7417 (p0) REVERT: A 1235 TRP cc_start: 0.8009 (p-90) cc_final: 0.7724 (p-90) REVERT: A 1263 ASN cc_start: 0.7771 (p0) cc_final: 0.7545 (p0) REVERT: A 1314 MET cc_start: 0.6578 (ttp) cc_final: 0.6240 (ttp) REVERT: A 1505 ASP cc_start: 0.7758 (t0) cc_final: 0.7531 (t0) REVERT: A 1511 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7034 (tm-30) REVERT: A 1515 SER cc_start: 0.8065 (p) cc_final: 0.7769 (p) REVERT: A 1957 TRP cc_start: 0.8540 (t-100) cc_final: 0.8271 (t-100) REVERT: A 1959 LYS cc_start: 0.8233 (ttmm) cc_final: 0.8021 (ttmm) REVERT: A 2024 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8129 (mtm110) REVERT: A 2052 ASP cc_start: 0.7821 (t70) cc_final: 0.7436 (t70) REVERT: A 2072 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.5853 (pt0) REVERT: A 2086 MET cc_start: 0.1359 (ptp) cc_final: -0.0559 (ptp) REVERT: A 2102 MET cc_start: 0.3054 (ppp) cc_final: 0.2680 (pp-130) REVERT: A 2176 MET cc_start: 0.5946 (tpt) cc_final: 0.5681 (tpt) REVERT: A 2178 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7159 (pmm) REVERT: A 2211 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8011 (pp) REVERT: A 2237 SER cc_start: 0.6910 (OUTLIER) cc_final: 0.6113 (m) REVERT: A 2520 LYS cc_start: 0.7720 (mttt) cc_final: 0.7471 (mttt) REVERT: A 2544 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 2630 ASN cc_start: 0.8173 (t0) cc_final: 0.7887 (t0) REVERT: A 2633 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7154 (tm-30) REVERT: A 2637 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7916 (mtpp) REVERT: A 2640 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: A 2689 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7216 (tpp) REVERT: A 2753 THR cc_start: 0.6721 (m) cc_final: 0.6402 (m) REVERT: A 2760 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.6563 (pm20) REVERT: B 21 ARG cc_start: 0.8397 (mmp80) cc_final: 0.8180 (mmp80) REVERT: B 28 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8291 (ttmm) REVERT: B 44 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6906 (mm-30) REVERT: B 401 TYR cc_start: 0.7290 (t80) cc_final: 0.7031 (t80) REVERT: B 501 GLN cc_start: 0.7812 (mt0) cc_final: 0.7459 (mt0) REVERT: B 505 MET cc_start: 0.6763 (mmm) cc_final: 0.6340 (mmm) REVERT: B 507 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 649 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6607 (tm-30) REVERT: B 651 TRP cc_start: 0.8549 (m-10) cc_final: 0.8266 (m-10) REVERT: B 655 GLU cc_start: 0.7732 (mp0) cc_final: 0.7513 (mp0) REVERT: B 822 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8329 (mmm) REVERT: B 834 ASP cc_start: 0.7534 (p0) cc_final: 0.7162 (p0) REVERT: B 884 ASP cc_start: 0.7861 (m-30) cc_final: 0.7445 (t0) REVERT: B 885 TYR cc_start: 0.8482 (t80) cc_final: 0.8169 (t80) REVERT: B 1082 LYS cc_start: 0.7791 (pptt) cc_final: 0.7513 (pptt) REVERT: B 1094 ASP cc_start: 0.7559 (m-30) cc_final: 0.7338 (m-30) REVERT: B 1143 GLU cc_start: 0.6865 (tp30) cc_final: 0.6640 (tp30) REVERT: B 1148 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 1366 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.4991 (tp30) REVERT: B 1511 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7083 (tm-30) REVERT: B 1833 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: B 2166 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8558 (tm) REVERT: B 2301 GLN cc_start: 0.8447 (tt0) cc_final: 0.8199 (mt0) REVERT: B 2303 PHE cc_start: 0.8450 (m-80) cc_final: 0.8047 (m-80) REVERT: B 2562 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8185 (ttpp) REVERT: B 2563 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8554 (m) REVERT: B 2565 TRP cc_start: 0.8181 (t60) cc_final: 0.7663 (t60) REVERT: B 2575 MET cc_start: 0.6808 (tpp) cc_final: 0.6502 (tpp) REVERT: B 2598 MET cc_start: 0.7266 (ptp) cc_final: 0.7060 (ptp) REVERT: B 2649 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: B 2708 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6646 (mm) REVERT: B 2723 MET cc_start: 0.7218 (tpp) cc_final: 0.6569 (tpp) REVERT: B 2743 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7711 (mt-10) outliers start: 181 outliers final: 97 residues processed: 734 average time/residue: 1.2573 time to fit residues: 1081.0459 Evaluate side-chains 723 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 605 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR 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 433 ARG Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 653 LEU 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 788 SER Chi-restraints excluded: chain A residue 818 THR 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 917 ASP Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1164 ASN 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 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 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 2024 ARG 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 2306 ASN Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2567 ASP Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2623 ASN Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2665 ASN Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2708 LEU Chi-restraints excluded: chain A residue 2717 ILE Chi-restraints excluded: chain A residue 2760 GLN 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 43 LEU Chi-restraints excluded: chain B residue 354 VAL 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 572 CYS 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 822 MET Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 936 LYS 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 1366 GLU Chi-restraints excluded: chain B residue 1507 MET Chi-restraints excluded: chain B residue 1512 GLU 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 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 2306 ASN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 6.9990 chunk 229 optimal weight: 0.5980 chunk 158 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 0.0980 chunk 324 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 290 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 HIS A1373 GLN A1720 ASN A1962 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2587 GLN ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 780 GLN B 782 ASN B 794 GLN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1508 GLN ** B1929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS ** B2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27152 Z= 0.187 Angle : 0.572 10.518 36788 Z= 0.282 Chirality : 0.040 0.190 4144 Planarity : 0.005 0.061 4762 Dihedral : 6.488 81.840 3739 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 5.95 % Allowed : 18.02 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3326 helix: 1.54 (0.14), residues: 1446 sheet: 0.49 (0.31), residues: 296 loop : -0.66 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 765 HIS 0.005 0.001 HIS B 849 PHE 0.036 0.001 PHE A1087 TYR 0.019 0.001 TYR B 768 ARG 0.009 0.000 ARG A2257 *********************** 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 799 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 622 time to evaluate : 3.097 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: 0.7613 (mp10) cc_final: 0.6983 (mp10) REVERT: A 49 LYS cc_start: 0.8641 (tptt) cc_final: 0.8095 (tppp) REVERT: A 75 GLN cc_start: 0.7944 (pm20) cc_final: 0.6590 (pp30) REVERT: A 361 GLN cc_start: 0.8105 (pt0) cc_final: 0.7819 (pt0) REVERT: A 426 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6939 (mm) REVERT: A 433 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6702 (ttm-80) REVERT: A 494 TRP cc_start: 0.7673 (p-90) cc_final: 0.7376 (p-90) REVERT: A 736 LYS cc_start: 0.7912 (ptmm) cc_final: 0.7431 (ptpp) REVERT: A 767 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7840 (mtm-85) REVERT: A 822 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8371 (mmp) REVERT: A 848 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7613 (t) REVERT: A 872 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7188 (mp0) REVERT: A 875 THR cc_start: 0.7964 (p) cc_final: 0.7649 (p) REVERT: A 889 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7814 (tmm-80) REVERT: A 890 GLN cc_start: 0.8109 (mm-40) cc_final: 0.6978 (mm-40) REVERT: A 894 ASN cc_start: 0.8501 (m110) cc_final: 0.8169 (m110) REVERT: A 1090 LYS cc_start: 0.8273 (ttmm) cc_final: 0.7938 (tppp) REVERT: A 1103 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7125 (tmt170) REVERT: A 1193 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 1222 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7626 (mtmm) REVERT: A 1233 ASP cc_start: 0.7698 (p0) cc_final: 0.7349 (p0) REVERT: A 1235 TRP cc_start: 0.8004 (p-90) cc_final: 0.7728 (p-90) REVERT: A 1263 ASN cc_start: 0.7741 (p0) cc_final: 0.7507 (p0) REVERT: A 1314 MET cc_start: 0.6587 (ttp) cc_final: 0.6242 (ttp) REVERT: A 1405 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7952 (mp) REVERT: A 1505 ASP cc_start: 0.7750 (t0) cc_final: 0.7537 (t0) REVERT: A 1511 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 1515 SER cc_start: 0.8071 (p) cc_final: 0.7752 (p) REVERT: A 1881 ARG cc_start: 0.2742 (OUTLIER) cc_final: 0.2009 (mpp-170) REVERT: A 1957 TRP cc_start: 0.8528 (t-100) cc_final: 0.8247 (t-100) REVERT: A 1959 LYS cc_start: 0.8252 (ttmm) cc_final: 0.8040 (ttmm) REVERT: A 2024 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8120 (mtm110) REVERT: A 2052 ASP cc_start: 0.7805 (t70) cc_final: 0.7378 (t70) REVERT: A 2072 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6679 (pt0) REVERT: A 2102 MET cc_start: 0.3021 (ppp) cc_final: 0.2645 (pp-130) REVERT: A 2176 MET cc_start: 0.5968 (tpt) cc_final: 0.5706 (tpt) REVERT: A 2178 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7124 (pmm) REVERT: A 2211 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 2275 HIS cc_start: 0.6515 (t-90) cc_final: 0.6311 (t-90) REVERT: A 2520 LYS cc_start: 0.7679 (mttt) cc_final: 0.7414 (mttt) REVERT: A 2544 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7420 (mm-30) REVERT: A 2630 ASN cc_start: 0.8193 (t0) cc_final: 0.7890 (t0) REVERT: A 2633 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 2637 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7862 (mtpp) REVERT: A 2640 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 2689 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7183 (tpp) REVERT: A 2760 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.6526 (pm20) REVERT: A 2774 VAL cc_start: 0.8429 (m) cc_final: 0.8179 (p) REVERT: B 21 ARG cc_start: 0.8365 (mmp80) cc_final: 0.8164 (mmp80) REVERT: B 28 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8276 (ttmm) REVERT: B 44 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6913 (mm-30) REVERT: B 63 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: B 501 GLN cc_start: 0.7789 (mt0) cc_final: 0.7444 (mt0) REVERT: B 505 MET cc_start: 0.6760 (mmm) cc_final: 0.6329 (mmm) REVERT: B 507 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7695 (mm-30) REVERT: B 649 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6521 (tm-30) REVERT: B 655 GLU cc_start: 0.7726 (mp0) cc_final: 0.7521 (mp0) REVERT: B 822 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8289 (mmm) REVERT: B 834 ASP cc_start: 0.7553 (p0) cc_final: 0.7184 (p0) REVERT: B 884 ASP cc_start: 0.7847 (m-30) cc_final: 0.7433 (t0) REVERT: B 885 TYR cc_start: 0.8469 (t80) cc_final: 0.8165 (t80) REVERT: B 1082 LYS cc_start: 0.7775 (pptt) cc_final: 0.7541 (pptt) REVERT: B 1094 ASP cc_start: 0.7536 (m-30) cc_final: 0.7327 (m-30) REVERT: B 1143 GLU cc_start: 0.6850 (tp30) cc_final: 0.6607 (tp30) REVERT: B 1511 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7109 (tm-30) REVERT: B 1833 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: B 1931 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 1959 LYS cc_start: 0.8313 (ttmm) cc_final: 0.8059 (ttmm) REVERT: B 2027 ASP cc_start: 0.7657 (t0) cc_final: 0.7341 (t0) REVERT: B 2166 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8557 (tm) REVERT: B 2301 GLN cc_start: 0.8404 (tt0) cc_final: 0.8179 (mt0) REVERT: B 2543 ASN cc_start: 0.8363 (t0) cc_final: 0.8146 (t0) REVERT: B 2562 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8186 (ttpp) REVERT: B 2563 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8557 (m) REVERT: B 2565 TRP cc_start: 0.8130 (t60) cc_final: 0.7645 (t60) REVERT: B 2575 MET cc_start: 0.6823 (tpp) cc_final: 0.6478 (tpp) REVERT: B 2649 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: B 2708 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6666 (mm) REVERT: B 2723 MET cc_start: 0.7146 (tpp) cc_final: 0.6350 (tpp) REVERT: B 2743 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7766 (mt-10) outliers start: 177 outliers final: 92 residues processed: 727 average time/residue: 1.2682 time to fit residues: 1079.9464 Evaluate side-chains 717 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 601 time to evaluate : 3.059 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 734 THR 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 818 THR 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 917 ASP Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1103 ARG Chi-restraints excluded: chain A residue 1164 ASN 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 1350 ASN Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1405 LEU 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 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 2024 ARG 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 2178 MET Chi-restraints excluded: chain A residue 2211 ILE Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2306 ASN 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 2623 ASN Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2708 LEU Chi-restraints excluded: chain A residue 2746 PHE Chi-restraints excluded: chain A residue 2760 GLN Chi-restraints excluded: chain A residue 2769 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 423 LYS 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 572 CYS 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 822 MET Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 1164 ASN 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 1507 MET 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 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 2306 ASN 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 270 optimal weight: 0.4980 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 291 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN A 914 HIS A 919 ASN A1411 ASN A1720 ASN A1962 ASN A2093 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 780 GLN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS ** B2093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27152 Z= 0.227 Angle : 0.585 10.949 36788 Z= 0.286 Chirality : 0.041 0.191 4144 Planarity : 0.005 0.061 4762 Dihedral : 6.173 82.983 3730 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.62 % Rotamer: Outliers : 6.22 % Allowed : 18.90 % Favored : 74.88 % 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: 0.61 (0.15), residues: 3326 helix: 1.58 (0.14), residues: 1434 sheet: 0.53 (0.30), residues: 306 loop : -0.71 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 765 HIS 0.005 0.001 HIS B1946 PHE 0.016 0.001 PHE A1917 TYR 0.023 0.001 TYR A2506 ARG 0.009 0.000 ARG A 767 *********************** 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 797 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 612 time to evaluate : 3.198 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: 0.7626 (mp10) cc_final: 0.7106 (mp10) REVERT: A 49 LYS cc_start: 0.8653 (tptt) cc_final: 0.8191 (mmmm) REVERT: A 75 GLN cc_start: 0.7940 (pm20) cc_final: 0.6575 (pp30) REVERT: A 361 GLN cc_start: 0.8068 (pt0) cc_final: 0.7748 (pt0) REVERT: A 426 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6956 (mm) REVERT: A 433 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.5543 (ttt90) REVERT: A 494 TRP cc_start: 0.7670 (p-90) cc_final: 0.7215 (p-90) REVERT: A 736 LYS cc_start: 0.7893 (ptmm) cc_final: 0.7429 (ptpp) REVERT: A 767 ARG cc_start: 0.7831 (mtm180) cc_final: 0.7478 (mtm-85) REVERT: A 822 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8393 (mmp) REVERT: A 848 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7625 (t) REVERT: A 872 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7197 (mp0) REVERT: A 875 THR cc_start: 0.7973 (p) cc_final: 0.7661 (p) REVERT: A 889 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7846 (tmm-80) REVERT: A 890 GLN cc_start: 0.8127 (mm-40) cc_final: 0.6873 (mm-40) REVERT: A 894 ASN cc_start: 0.8508 (m110) cc_final: 0.8174 (m110) REVERT: A 1090 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7967 (tppp) REVERT: A 1103 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7173 (tmt170) REVERT: A 1193 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8357 (mp) REVERT: A 1235 TRP cc_start: 0.8025 (p-90) cc_final: 0.7737 (p-90) REVERT: A 1253 ASP cc_start: 0.7681 (t0) cc_final: 0.7362 (t0) REVERT: A 1263 ASN cc_start: 0.7756 (p0) cc_final: 0.7504 (p0) REVERT: A 1314 MET cc_start: 0.6594 (ttp) cc_final: 0.6245 (ttp) REVERT: A 1505 ASP cc_start: 0.7749 (t0) cc_final: 0.7535 (t0) REVERT: A 1511 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7076 (tm-30) REVERT: A 1515 SER cc_start: 0.8084 (p) cc_final: 0.7762 (p) REVERT: A 1957 TRP cc_start: 0.8532 (t-100) cc_final: 0.8262 (t-100) REVERT: A 1959 LYS cc_start: 0.8230 (ttmm) cc_final: 0.8012 (ttmm) REVERT: A 2024 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8118 (mtm110) REVERT: A 2052 ASP cc_start: 0.7779 (t70) cc_final: 0.7354 (t70) REVERT: A 2072 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.5975 (pt0) REVERT: A 2102 MET cc_start: 0.2988 (ppp) cc_final: 0.2593 (pp-130) REVERT: A 2176 MET cc_start: 0.5980 (tpt) cc_final: 0.5715 (tpt) REVERT: A 2178 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7140 (pmm) REVERT: A 2211 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8028 (pp) REVERT: A 2227 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6900 (tpp-160) REVERT: A 2237 SER cc_start: 0.6817 (OUTLIER) cc_final: 0.6084 (m) REVERT: A 2275 HIS cc_start: 0.6515 (t-90) cc_final: 0.6299 (t-90) REVERT: A 2520 LYS cc_start: 0.7690 (mttt) cc_final: 0.7417 (mttt) REVERT: A 2544 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7430 (mm-30) REVERT: A 2630 ASN cc_start: 0.8167 (t0) cc_final: 0.7849 (t0) REVERT: A 2633 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7051 (tm-30) REVERT: A 2637 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7761 (mttm) REVERT: A 2640 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: A 2689 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7237 (tpp) REVERT: A 2760 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.6481 (pm20) REVERT: B 27 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7373 (tm-30) REVERT: B 28 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8221 (ttmm) REVERT: B 45 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7719 (mp10) REVERT: B 501 GLN cc_start: 0.7796 (mt0) cc_final: 0.7455 (mt0) REVERT: B 505 MET cc_start: 0.6744 (mmm) cc_final: 0.6302 (mmm) REVERT: B 655 GLU cc_start: 0.7732 (mp0) cc_final: 0.7505 (mp0) REVERT: B 834 ASP cc_start: 0.7567 (p0) cc_final: 0.7196 (p0) REVERT: B 885 TYR cc_start: 0.8502 (t80) cc_final: 0.8238 (t80) REVERT: B 889 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7340 (mtm-85) REVERT: B 936 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7187 (mtmm) REVERT: B 1082 LYS cc_start: 0.7791 (pptt) cc_final: 0.7572 (pptt) REVERT: B 1094 ASP cc_start: 0.7553 (m-30) cc_final: 0.7331 (m-30) REVERT: B 1143 GLU cc_start: 0.6868 (tp30) cc_final: 0.6591 (tp30) REVERT: B 1233 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7187 (p0) REVERT: B 1511 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7120 (tm-30) REVERT: B 1691 LEU cc_start: -0.0427 (OUTLIER) cc_final: -0.1324 (mt) REVERT: B 1833 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: B 1959 LYS cc_start: 0.8329 (ttmm) cc_final: 0.8063 (ttmm) REVERT: B 2166 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8575 (tm) REVERT: B 2225 PHE cc_start: 0.8399 (t80) cc_final: 0.8188 (t80) REVERT: B 2301 GLN cc_start: 0.8430 (tt0) cc_final: 0.8201 (mt0) REVERT: B 2543 ASN cc_start: 0.8354 (t0) cc_final: 0.8118 (t0) REVERT: B 2562 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8196 (ttpp) REVERT: B 2563 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8569 (m) REVERT: B 2565 TRP cc_start: 0.8167 (t60) cc_final: 0.7665 (t60) REVERT: B 2575 MET cc_start: 0.6847 (tpp) cc_final: 0.6492 (tpp) REVERT: B 2649 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: B 2708 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6610 (mm) REVERT: B 2723 MET cc_start: 0.7173 (tpp) cc_final: 0.6438 (tpp) REVERT: B 2743 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 2762 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4540 (pt) outliers start: 185 outliers final: 104 residues processed: 724 average time/residue: 1.2653 time to fit residues: 1075.5440 Evaluate side-chains 726 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 594 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR 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 390 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 562 MET 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 734 THR 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 794 GLN 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 917 ASP Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1103 ARG Chi-restraints excluded: chain A residue 1164 ASN 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 1350 ASN 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 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 2024 ARG Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2030 THR 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 2178 MET 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 2245 ASP Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2548 ILE Chi-restraints excluded: chain A residue 2567 ASP Chi-restraints excluded: chain A residue 2623 ASN Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2665 ASN Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2708 LEU Chi-restraints excluded: chain A residue 2746 PHE Chi-restraints excluded: chain A residue 2760 GLN 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 390 LEU Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 547 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 572 CYS Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 773 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 836 LEU Chi-restraints excluded: chain B residue 889 ARG Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 936 LYS Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1164 ASN Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1233 ASP 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 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 1697 ARG 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 2166 LEU Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2306 ASN 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 2708 LEU Chi-restraints excluded: chain B residue 2722 SER 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 109 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 325 optimal weight: 1.9990 chunk 269 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1411 ASN A1720 ASN A1962 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 780 GLN B 794 GLN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS B2093 ASN ** B2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 27152 Z= 0.360 Angle : 0.637 10.294 36788 Z= 0.315 Chirality : 0.044 0.264 4144 Planarity : 0.005 0.073 4762 Dihedral : 6.262 85.018 3725 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 6.39 % Allowed : 19.37 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3326 helix: 1.39 (0.14), residues: 1438 sheet: 0.37 (0.30), residues: 308 loop : -0.81 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 765 HIS 0.008 0.001 HIS A1946 PHE 0.031 0.002 PHE B2675 TYR 0.018 0.002 TYR B 482 ARG 0.009 0.001 ARG A2755 *********************** 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 807 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 617 time to evaluate : 2.952 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: 0.7685 (mp10) cc_final: 0.7161 (mp10) REVERT: A 49 LYS cc_start: 0.8651 (tptt) cc_final: 0.8203 (mmmm) REVERT: A 75 GLN cc_start: 0.7980 (pm20) cc_final: 0.6614 (pp30) REVERT: A 361 GLN cc_start: 0.8048 (pt0) cc_final: 0.7774 (pt0) REVERT: A 392 GLN cc_start: 0.7546 (pp30) cc_final: 0.6899 (pt0) REVERT: A 426 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6972 (mm) REVERT: A 433 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.5687 (ttt90) REVERT: A 494 TRP cc_start: 0.7727 (p-90) cc_final: 0.7279 (p-90) REVERT: A 736 LYS cc_start: 0.7936 (ptmm) cc_final: 0.7457 (ptpp) REVERT: A 822 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8365 (mmp) REVERT: A 875 THR cc_start: 0.7903 (p) cc_final: 0.7612 (p) REVERT: A 889 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7978 (tmm-80) REVERT: A 894 ASN cc_start: 0.8525 (m110) cc_final: 0.8181 (m110) REVERT: A 1090 LYS cc_start: 0.8333 (ttmm) cc_final: 0.7962 (tppp) REVERT: A 1103 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7257 (tmt170) REVERT: A 1222 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7697 (mmmm) REVERT: A 1253 ASP cc_start: 0.7683 (t0) cc_final: 0.7378 (t0) REVERT: A 1263 ASN cc_start: 0.7808 (p0) cc_final: 0.7557 (p0) REVERT: A 1314 MET cc_start: 0.6595 (ttp) cc_final: 0.6251 (ttp) REVERT: A 1505 ASP cc_start: 0.7779 (t0) cc_final: 0.7569 (t0) REVERT: A 1511 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7224 (tm-30) REVERT: A 1515 SER cc_start: 0.8099 (p) cc_final: 0.7701 (p) REVERT: A 1957 TRP cc_start: 0.8563 (t-100) cc_final: 0.8309 (t-100) REVERT: A 1959 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7973 (ttmm) REVERT: A 2024 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8079 (mtm110) REVERT: A 2052 ASP cc_start: 0.7830 (t70) cc_final: 0.7420 (t70) REVERT: A 2086 MET cc_start: 0.3709 (OUTLIER) cc_final: 0.3040 (mtm) REVERT: A 2102 MET cc_start: 0.3128 (ppp) cc_final: 0.2725 (pp-130) REVERT: A 2176 MET cc_start: 0.5994 (tpt) cc_final: 0.5715 (tpt) REVERT: A 2178 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7176 (pmm) REVERT: A 2211 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8054 (pp) REVERT: A 2227 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6974 (tpp-160) REVERT: A 2237 SER cc_start: 0.6851 (OUTLIER) cc_final: 0.6137 (m) REVERT: A 2275 HIS cc_start: 0.6542 (t-90) cc_final: 0.6336 (t-90) REVERT: A 2520 LYS cc_start: 0.7726 (mttt) cc_final: 0.7444 (mttt) REVERT: A 2544 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 2630 ASN cc_start: 0.8251 (t0) cc_final: 0.7959 (t0) REVERT: A 2633 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 2637 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7907 (mtpm) REVERT: A 2640 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: A 2689 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7182 (tpp) REVERT: A 2760 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.6622 (pm20) REVERT: B 27 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 28 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8243 (ttmm) REVERT: B 45 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: B 63 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 501 GLN cc_start: 0.7838 (mt0) cc_final: 0.7502 (mt0) REVERT: B 505 MET cc_start: 0.6783 (mmm) cc_final: 0.6342 (mmm) REVERT: B 834 ASP cc_start: 0.7584 (p0) cc_final: 0.7208 (p0) REVERT: B 885 TYR cc_start: 0.8593 (t80) cc_final: 0.8365 (t80) REVERT: B 1082 LYS cc_start: 0.7838 (pptt) cc_final: 0.7606 (pptt) REVERT: B 1094 ASP cc_start: 0.7576 (m-30) cc_final: 0.7364 (m-30) REVERT: B 1096 VAL cc_start: 0.9258 (p) cc_final: 0.9035 (t) REVERT: B 1233 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7360 (p0) REVERT: B 1263 ASN cc_start: 0.7914 (p0) cc_final: 0.7659 (p0) REVERT: B 1511 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7129 (tm-30) REVERT: B 1691 LEU cc_start: -0.0320 (OUTLIER) cc_final: -0.1223 (mt) REVERT: B 1833 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: B 2225 PHE cc_start: 0.8433 (t80) cc_final: 0.8221 (t80) REVERT: B 2301 GLN cc_start: 0.8464 (tt0) cc_final: 0.8202 (mt0) REVERT: B 2562 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8170 (ttpp) REVERT: B 2563 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8584 (m) REVERT: B 2575 MET cc_start: 0.6856 (tpp) cc_final: 0.6514 (tpp) REVERT: B 2598 MET cc_start: 0.7370 (ptp) cc_final: 0.7024 (ppp) REVERT: B 2649 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: B 2708 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6777 (mm) REVERT: B 2723 MET cc_start: 0.7276 (tpp) cc_final: 0.6497 (tpp) REVERT: B 2743 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 2762 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4448 (pt) outliers start: 190 outliers final: 113 residues processed: 732 average time/residue: 1.2409 time to fit residues: 1066.0945 Evaluate side-chains 738 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 602 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR 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 433 ARG Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 562 MET 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 734 THR 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 818 THR 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 1103 ARG Chi-restraints excluded: chain A residue 1164 ASN 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 1350 ASN 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 1516 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 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 2024 ARG Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2030 THR 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 2178 MET 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 2245 ASP Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2306 ASN 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 2623 ASN Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2717 ILE Chi-restraints excluded: chain A residue 2724 THR Chi-restraints excluded: chain A residue 2760 GLN 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 390 LEU Chi-restraints excluded: chain B residue 423 LYS 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 572 CYS Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 769 CYS 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 812 LEU Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1164 ASN Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1229 THR Chi-restraints excluded: chain B residue 1231 TYR Chi-restraints excluded: chain B residue 1233 ASP 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 1347 SER Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1404 THR 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 1697 ARG Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1718 VAL Chi-restraints excluded: chain B residue 1801 LEU 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 1952 GLN Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2306 ASN 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 2667 LEU Chi-restraints excluded: chain B residue 2677 LEU Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2722 SER Chi-restraints excluded: chain B residue 2762 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 237 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 323 optimal weight: 0.9980 chunk 202 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1411 ASN A1720 ASN A1962 ASN A2093 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS B 489 ASN B 794 GLN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1929 ASN B1932 HIS ** B2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27152 Z= 0.228 Angle : 0.615 10.761 36788 Z= 0.301 Chirality : 0.041 0.223 4144 Planarity : 0.005 0.064 4762 Dihedral : 6.083 82.567 3720 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 5.65 % Allowed : 20.88 % 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: 0.52 (0.15), residues: 3326 helix: 1.47 (0.14), residues: 1448 sheet: 0.48 (0.30), residues: 306 loop : -0.74 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 765 HIS 0.007 0.001 HIS B 849 PHE 0.035 0.002 PHE A1087 TYR 0.030 0.002 TYR B 401 ARG 0.009 0.000 ARG B2233 *********************** 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 784 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 616 time to evaluate : 2.952 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: 0.7665 (mp10) cc_final: 0.7050 (mp10) REVERT: A 49 LYS cc_start: 0.8652 (tptt) cc_final: 0.8192 (mmmm) REVERT: A 75 GLN cc_start: 0.7959 (pm20) cc_final: 0.6610 (pp30) REVERT: A 361 GLN cc_start: 0.8038 (pt0) cc_final: 0.7749 (pt0) REVERT: A 392 GLN cc_start: 0.7484 (pp30) cc_final: 0.6875 (pt0) REVERT: A 426 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6954 (mm) REVERT: A 433 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.5567 (ttt90) REVERT: A 494 TRP cc_start: 0.7680 (p-90) cc_final: 0.7236 (p-90) REVERT: A 736 LYS cc_start: 0.7887 (ptmm) cc_final: 0.7406 (ptpp) REVERT: A 822 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8391 (mmp) REVERT: A 872 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7050 (mp0) REVERT: A 875 THR cc_start: 0.7864 (p) cc_final: 0.7575 (p) REVERT: A 889 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7844 (tmm-80) REVERT: A 890 GLN cc_start: 0.8153 (mm-40) cc_final: 0.6955 (mm-40) REVERT: A 894 ASN cc_start: 0.8516 (m110) cc_final: 0.8174 (m110) REVERT: A 1090 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7938 (tppp) REVERT: A 1139 ILE cc_start: 0.8604 (mt) cc_final: 0.8384 (mp) REVERT: A 1222 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7768 (mmmm) REVERT: A 1263 ASN cc_start: 0.7776 (p0) cc_final: 0.7513 (p0) REVERT: A 1314 MET cc_start: 0.6586 (ttp) cc_final: 0.6245 (ttp) REVERT: A 1505 ASP cc_start: 0.7766 (t0) cc_final: 0.7559 (t0) REVERT: A 1511 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 1515 SER cc_start: 0.8101 (p) cc_final: 0.7705 (p) REVERT: A 1957 TRP cc_start: 0.8555 (t-100) cc_final: 0.8267 (t-100) REVERT: A 1959 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7927 (ttmm) REVERT: A 2024 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8071 (mtm110) REVERT: A 2052 ASP cc_start: 0.7782 (t70) cc_final: 0.7397 (t70) REVERT: A 2102 MET cc_start: 0.3086 (ppp) cc_final: 0.2711 (pp-130) REVERT: A 2176 MET cc_start: 0.5988 (tpt) cc_final: 0.5708 (tpt) REVERT: A 2178 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7149 (pmm) REVERT: A 2211 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8050 (pp) REVERT: A 2219 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7482 (mp0) REVERT: A 2237 SER cc_start: 0.6817 (OUTLIER) cc_final: 0.6100 (m) REVERT: A 2275 HIS cc_start: 0.6491 (t-90) cc_final: 0.6250 (t-90) REVERT: A 2520 LYS cc_start: 0.7697 (mttt) cc_final: 0.7337 (mttt) REVERT: A 2544 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 2630 ASN cc_start: 0.8208 (t0) cc_final: 0.7907 (t0) REVERT: A 2633 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 2637 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7820 (mtpp) REVERT: A 2640 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: A 2689 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7235 (tpp) REVERT: A 2753 THR cc_start: 0.6636 (m) cc_final: 0.6259 (p) REVERT: A 2760 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.6638 (pm20) REVERT: B 27 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 28 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8226 (ttmm) REVERT: B 45 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: B 63 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7299 (mm-30) REVERT: B 501 GLN cc_start: 0.7807 (mt0) cc_final: 0.7466 (mt0) REVERT: B 505 MET cc_start: 0.6699 (mmm) cc_final: 0.6338 (mmm) REVERT: B 834 ASP cc_start: 0.7568 (p0) cc_final: 0.7127 (p0) REVERT: B 885 TYR cc_start: 0.8533 (t80) cc_final: 0.8269 (t80) REVERT: B 1082 LYS cc_start: 0.7805 (pptt) cc_final: 0.7583 (pptt) REVERT: B 1094 ASP cc_start: 0.7550 (m-30) cc_final: 0.7346 (m-30) REVERT: B 1143 GLU cc_start: 0.6924 (tp30) cc_final: 0.6669 (tp30) REVERT: B 1263 ASN cc_start: 0.7901 (p0) cc_final: 0.7645 (p0) REVERT: B 1511 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7088 (tm-30) REVERT: B 1691 LEU cc_start: -0.0315 (OUTLIER) cc_final: -0.1165 (mt) REVERT: B 1825 VAL cc_start: 0.8498 (t) cc_final: 0.8151 (m) REVERT: B 1833 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: B 1959 LYS cc_start: 0.8316 (ttmm) cc_final: 0.8081 (ttmm) REVERT: B 2225 PHE cc_start: 0.8435 (t80) cc_final: 0.8234 (t80) REVERT: B 2301 GLN cc_start: 0.8424 (tt0) cc_final: 0.8140 (mt0) REVERT: B 2534 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7763 (mtt180) REVERT: B 2543 ASN cc_start: 0.8346 (t0) cc_final: 0.8128 (t0) REVERT: B 2562 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8195 (ttpp) REVERT: B 2563 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8618 (m) REVERT: B 2565 TRP cc_start: 0.8165 (t60) cc_final: 0.7592 (t60) REVERT: B 2575 MET cc_start: 0.6856 (tpp) cc_final: 0.6524 (tpp) REVERT: B 2598 MET cc_start: 0.7384 (ptp) cc_final: 0.6985 (ppp) REVERT: B 2708 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6790 (mm) REVERT: B 2723 MET cc_start: 0.7248 (tpp) cc_final: 0.6466 (tpp) REVERT: B 2743 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7787 (mt-10) REVERT: B 2762 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.4449 (pt) outliers start: 168 outliers final: 106 residues processed: 712 average time/residue: 1.2517 time to fit residues: 1047.3257 Evaluate side-chains 723 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 599 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 34 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 426 LEU Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 562 MET 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 818 THR 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 917 ASP Chi-restraints excluded: chain A residue 1118 MET Chi-restraints excluded: chain A residue 1164 ASN 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 1347 SER Chi-restraints excluded: chain A residue 1350 ASN 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 1833 GLU Chi-restraints excluded: chain A residue 1836 ILE Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2024 ARG 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 2166 LEU 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 2245 ASP Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2567 ASP Chi-restraints excluded: chain A residue 2623 ASN Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2724 THR Chi-restraints excluded: chain A residue 2760 GLN 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 390 LEU Chi-restraints excluded: chain B residue 423 LYS 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 572 CYS Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 769 CYS Chi-restraints excluded: chain B residue 773 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 836 LEU Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1164 ASN 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 1347 SER Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1404 THR Chi-restraints excluded: chain B residue 1405 LEU 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 1718 VAL Chi-restraints excluded: chain B residue 1789 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 1952 GLN Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2306 ASN 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 2627 THR Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2722 SER Chi-restraints excluded: chain B residue 2762 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.0670 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 254 optimal weight: 0.9980 overall best weight: 1.1722 ------------------------------------------------------------------------------- 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 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1411 ASN A1962 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1508 GLN B1932 HIS ** B2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27152 Z= 0.295 Angle : 0.641 12.347 36788 Z= 0.313 Chirality : 0.043 0.236 4144 Planarity : 0.005 0.068 4762 Dihedral : 6.044 83.979 3716 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.23 % Rotamer: Outliers : 5.45 % Allowed : 21.55 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3326 helix: 1.43 (0.14), residues: 1446 sheet: 0.44 (0.30), residues: 308 loop : -0.79 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 765 HIS 0.011 0.001 HIS A1807 PHE 0.033 0.002 PHE B2675 TYR 0.023 0.002 TYR B 401 ARG 0.010 0.000 ARG B2233 *********************** 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 766 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 604 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7694 (mp10) cc_final: 0.7062 (mp10) REVERT: A 49 LYS cc_start: 0.8643 (tptt) cc_final: 0.8196 (mmmm) REVERT: A 75 GLN cc_start: 0.7961 (pm20) cc_final: 0.6614 (pp30) REVERT: A 361 GLN cc_start: 0.8010 (pt0) cc_final: 0.7758 (pt0) REVERT: A 426 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6964 (mm) REVERT: A 433 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.5644 (ttt90) REVERT: A 494 TRP cc_start: 0.7700 (p-90) cc_final: 0.7214 (p-90) REVERT: A 736 LYS cc_start: 0.7913 (ptmm) cc_final: 0.7421 (ptpp) REVERT: A 822 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8401 (mmp) REVERT: A 875 THR cc_start: 0.7864 (p) cc_final: 0.7566 (p) REVERT: A 889 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8012 (tmm-80) REVERT: A 894 ASN cc_start: 0.8520 (m110) cc_final: 0.8174 (m110) REVERT: A 1090 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7941 (tppp) REVERT: A 1139 ILE cc_start: 0.8584 (mt) cc_final: 0.8363 (mp) REVERT: A 1222 LYS cc_start: 0.7990 (mmmm) cc_final: 0.7753 (mmmm) REVERT: A 1263 ASN cc_start: 0.7792 (p0) cc_final: 0.7510 (p0) REVERT: A 1314 MET cc_start: 0.6605 (ttp) cc_final: 0.6255 (ttp) REVERT: A 1511 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 1515 SER cc_start: 0.8111 (p) cc_final: 0.7713 (p) REVERT: A 1957 TRP cc_start: 0.8565 (t-100) cc_final: 0.8281 (t-100) REVERT: A 1959 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7966 (ttmm) REVERT: A 2024 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8072 (mtm110) REVERT: A 2052 ASP cc_start: 0.7815 (t70) cc_final: 0.7394 (t70) REVERT: A 2086 MET cc_start: 0.3566 (OUTLIER) cc_final: 0.2934 (mtm) REVERT: A 2102 MET cc_start: 0.3246 (ppp) cc_final: 0.2855 (pp-130) REVERT: A 2176 MET cc_start: 0.6013 (tpt) cc_final: 0.5713 (tpt) REVERT: A 2178 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7166 (pmm) REVERT: A 2211 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8068 (pp) REVERT: A 2219 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7494 (mp0) REVERT: A 2237 SER cc_start: 0.6829 (OUTLIER) cc_final: 0.6108 (m) REVERT: A 2275 HIS cc_start: 0.6495 (t-90) cc_final: 0.6256 (t-90) REVERT: A 2520 LYS cc_start: 0.7683 (mttt) cc_final: 0.7331 (mptt) REVERT: A 2544 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 2630 ASN cc_start: 0.8262 (t0) cc_final: 0.7894 (t0) REVERT: A 2633 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 2637 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7778 (mtpp) REVERT: A 2640 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: A 2689 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7206 (tpp) REVERT: A 2753 THR cc_start: 0.6677 (m) cc_final: 0.6260 (p) REVERT: A 2760 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: B 27 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 28 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8235 (ttmm) REVERT: B 45 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: B 63 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 501 GLN cc_start: 0.7828 (mt0) cc_final: 0.7491 (mt0) REVERT: B 505 MET cc_start: 0.6714 (mmm) cc_final: 0.6350 (mmm) REVERT: B 834 ASP cc_start: 0.7552 (p0) cc_final: 0.7114 (p0) REVERT: B 885 TYR cc_start: 0.8572 (t80) cc_final: 0.8354 (t80) REVERT: B 1082 LYS cc_start: 0.7821 (pptt) cc_final: 0.7590 (pptt) REVERT: B 1096 VAL cc_start: 0.9238 (p) cc_final: 0.9004 (t) REVERT: B 1143 GLU cc_start: 0.6968 (tp30) cc_final: 0.6701 (tp30) REVERT: B 1263 ASN cc_start: 0.7908 (p0) cc_final: 0.7667 (p0) REVERT: B 1511 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7089 (tm-30) REVERT: B 1691 LEU cc_start: -0.0327 (OUTLIER) cc_final: -0.1151 (mt) REVERT: B 1833 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: B 1959 LYS cc_start: 0.8326 (ttmm) cc_final: 0.8041 (ttmm) REVERT: B 2225 PHE cc_start: 0.8441 (t80) cc_final: 0.8183 (t80) REVERT: B 2301 GLN cc_start: 0.8453 (tt0) cc_final: 0.8176 (mt0) REVERT: B 2543 ASN cc_start: 0.8381 (t0) cc_final: 0.8169 (t0) REVERT: B 2562 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8201 (ttpp) REVERT: B 2563 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8635 (m) REVERT: B 2575 MET cc_start: 0.6892 (tpp) cc_final: 0.6550 (tpp) REVERT: B 2598 MET cc_start: 0.7358 (ptp) cc_final: 0.6996 (ppp) REVERT: B 2637 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7618 (mmmm) REVERT: B 2708 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6808 (mm) REVERT: B 2723 MET cc_start: 0.7269 (tpp) cc_final: 0.6538 (tpp) REVERT: B 2743 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7797 (mt-10) outliers start: 162 outliers final: 115 residues processed: 702 average time/residue: 1.2359 time to fit residues: 1017.6745 Evaluate side-chains 734 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 601 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 34 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 433 ARG Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 562 MET 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 734 THR 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 794 GLN Chi-restraints excluded: chain A residue 818 THR 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 1118 MET Chi-restraints excluded: chain A residue 1164 ASN 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 1235 TRP Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1347 SER Chi-restraints excluded: chain A residue 1350 ASN 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 1516 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 1789 SER Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 2024 ARG Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2030 THR Chi-restraints excluded: chain A residue 2086 MET 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 2245 ASP Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2567 ASP Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2618 ILE Chi-restraints excluded: chain A residue 2623 ASN Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2665 ASN Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2717 ILE Chi-restraints excluded: chain A residue 2724 THR Chi-restraints excluded: chain A residue 2760 GLN 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 390 LEU Chi-restraints excluded: chain B residue 423 LYS 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 572 CYS Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 769 CYS Chi-restraints excluded: chain B residue 773 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 836 LEU Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1164 ASN Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1229 THR 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 1347 SER Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1405 LEU 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 1697 ARG Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1718 VAL Chi-restraints excluded: chain B residue 1789 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 1952 GLN Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2306 ASN 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 2627 THR Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2722 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 236 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 285 optimal weight: 0.0030 chunk 300 optimal weight: 6.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** B2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27152 Z= 0.270 Angle : 0.645 12.124 36788 Z= 0.315 Chirality : 0.043 0.271 4144 Planarity : 0.005 0.068 4762 Dihedral : 6.012 83.176 3714 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.53 % Favored : 94.35 % Rotamer: Outliers : 5.14 % Allowed : 22.16 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3326 helix: 1.45 (0.14), residues: 1446 sheet: 0.47 (0.30), residues: 308 loop : -0.78 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 765 HIS 0.009 0.001 HIS A1807 PHE 0.035 0.002 PHE A1087 TYR 0.027 0.002 TYR A2506 ARG 0.010 0.000 ARG B2233 *********************** 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 764 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 611 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7669 (mp10) cc_final: 0.7016 (mp10) REVERT: A 49 LYS cc_start: 0.8646 (tptt) cc_final: 0.8198 (mmmm) REVERT: A 75 GLN cc_start: 0.7958 (pm20) cc_final: 0.6612 (pp30) REVERT: A 361 GLN cc_start: 0.7995 (pt0) cc_final: 0.7728 (pt0) REVERT: A 426 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6950 (mm) REVERT: A 433 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.5599 (ttt90) REVERT: A 494 TRP cc_start: 0.7700 (p-90) cc_final: 0.7217 (p-90) REVERT: A 736 LYS cc_start: 0.7908 (ptmm) cc_final: 0.7414 (ptpp) REVERT: A 822 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8404 (mmp) REVERT: A 875 THR cc_start: 0.7856 (p) cc_final: 0.7565 (p) REVERT: A 889 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7992 (tmm-80) REVERT: A 894 ASN cc_start: 0.8508 (m110) cc_final: 0.8164 (m110) REVERT: A 1090 LYS cc_start: 0.8333 (ttmm) cc_final: 0.7967 (tppp) REVERT: A 1139 ILE cc_start: 0.8599 (mt) cc_final: 0.8377 (mp) REVERT: A 1222 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7774 (mmmm) REVERT: A 1263 ASN cc_start: 0.7787 (p0) cc_final: 0.7499 (p0) REVERT: A 1314 MET cc_start: 0.6614 (ttp) cc_final: 0.6256 (ttp) REVERT: A 1488 MET cc_start: 0.8659 (ttp) cc_final: 0.8440 (ttm) REVERT: A 1511 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 1515 SER cc_start: 0.8116 (p) cc_final: 0.7717 (p) REVERT: A 1833 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: A 1881 ARG cc_start: 0.3126 (OUTLIER) cc_final: 0.2841 (mtt180) REVERT: A 1957 TRP cc_start: 0.8571 (t-100) cc_final: 0.8257 (t-100) REVERT: A 1959 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7955 (ttmm) REVERT: A 2024 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8065 (mtm110) REVERT: A 2052 ASP cc_start: 0.7786 (t70) cc_final: 0.7404 (t70) REVERT: A 2102 MET cc_start: 0.3355 (ppp) cc_final: 0.2940 (pp-130) REVERT: A 2176 MET cc_start: 0.6010 (tpt) cc_final: 0.5715 (tpt) REVERT: A 2178 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7162 (pmm) REVERT: A 2211 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8064 (pp) REVERT: A 2219 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7538 (mp0) REVERT: A 2237 SER cc_start: 0.6805 (OUTLIER) cc_final: 0.6077 (m) REVERT: A 2275 HIS cc_start: 0.6484 (t-90) cc_final: 0.6251 (t-90) REVERT: A 2520 LYS cc_start: 0.7668 (mttt) cc_final: 0.7318 (mptt) REVERT: A 2544 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 2575 MET cc_start: 0.8150 (tpp) cc_final: 0.7912 (tpt) REVERT: A 2630 ASN cc_start: 0.8256 (t0) cc_final: 0.7887 (t0) REVERT: A 2633 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 2637 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7765 (mtpp) REVERT: A 2640 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 2689 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7239 (tpp) REVERT: A 2753 THR cc_start: 0.6664 (m) cc_final: 0.6250 (p) REVERT: A 2760 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6626 (pm20) REVERT: B 27 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 28 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8240 (ttmm) REVERT: B 45 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: B 63 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 417 LEU cc_start: 0.8418 (mt) cc_final: 0.8154 (mt) REVERT: B 501 GLN cc_start: 0.7818 (mt0) cc_final: 0.7482 (mt0) REVERT: B 505 MET cc_start: 0.6696 (mmm) cc_final: 0.6341 (mmm) REVERT: B 507 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7778 (mm-30) REVERT: B 834 ASP cc_start: 0.7554 (p0) cc_final: 0.7109 (p0) REVERT: B 885 TYR cc_start: 0.8554 (t80) cc_final: 0.8311 (t80) REVERT: B 1082 LYS cc_start: 0.7813 (pptt) cc_final: 0.7600 (pptt) REVERT: B 1090 LYS cc_start: 0.8559 (tppp) cc_final: 0.8356 (tppp) REVERT: B 1096 VAL cc_start: 0.9252 (p) cc_final: 0.9022 (t) REVERT: B 1143 GLU cc_start: 0.6979 (tp30) cc_final: 0.6712 (tp30) REVERT: B 1263 ASN cc_start: 0.7896 (p0) cc_final: 0.7651 (p0) REVERT: B 1511 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 1691 LEU cc_start: -0.0334 (OUTLIER) cc_final: -0.1187 (mt) REVERT: B 1825 VAL cc_start: 0.8513 (t) cc_final: 0.8156 (m) REVERT: B 1833 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: B 1959 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8032 (ttmm) REVERT: B 2225 PHE cc_start: 0.8420 (t80) cc_final: 0.8162 (t80) REVERT: B 2301 GLN cc_start: 0.8436 (tt0) cc_final: 0.8169 (mt0) REVERT: B 2543 ASN cc_start: 0.8375 (t0) cc_final: 0.8157 (t0) REVERT: B 2562 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8199 (ttpp) REVERT: B 2563 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8643 (m) REVERT: B 2575 MET cc_start: 0.6893 (tpp) cc_final: 0.6559 (tpp) REVERT: B 2598 MET cc_start: 0.7378 (ptp) cc_final: 0.7030 (ppp) REVERT: B 2637 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7568 (mmmm) REVERT: B 2708 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6818 (mm) REVERT: B 2723 MET cc_start: 0.7278 (tpp) cc_final: 0.6515 (tpp) REVERT: B 2743 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7793 (mt-10) outliers start: 153 outliers final: 111 residues processed: 701 average time/residue: 1.2819 time to fit residues: 1054.5997 Evaluate side-chains 728 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 598 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 34 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 433 ARG Chi-restraints excluded: chain A residue 445 THR 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 734 THR 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 818 THR 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 917 ASP Chi-restraints excluded: chain A residue 1118 MET Chi-restraints excluded: chain A residue 1164 ASN 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 1235 TRP Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1347 SER Chi-restraints excluded: chain A residue 1350 ASN Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1516 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 1789 SER 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 2024 ARG Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2030 THR 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 2245 ASP Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2567 ASP Chi-restraints excluded: chain A residue 2582 LEU Chi-restraints excluded: chain A residue 2618 ILE Chi-restraints excluded: chain A residue 2623 ASN Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2665 ASN Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2724 THR Chi-restraints excluded: chain A residue 2760 GLN 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 423 LYS Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 479 CYS 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 572 CYS Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 769 CYS Chi-restraints excluded: chain B residue 773 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 836 LEU Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 1164 ASN Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1229 THR 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 1347 SER Chi-restraints excluded: chain B residue 1377 THR 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 1697 ARG Chi-restraints excluded: chain B residue 1698 THR Chi-restraints excluded: chain B residue 1718 VAL Chi-restraints excluded: chain B residue 1789 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 1952 GLN Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2306 ASN Chi-restraints excluded: chain B residue 2506 TYR 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 2627 THR Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2722 SER Chi-restraints excluded: chain B residue 2749 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 4.9990 chunk 319 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 221 optimal weight: 0.0970 chunk 334 optimal weight: 2.9990 chunk 308 optimal weight: 0.0020 chunk 266 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1411 ASN A1962 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1929 ASN B1932 HIS ** B2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27152 Z= 0.226 Angle : 0.652 12.604 36788 Z= 0.316 Chirality : 0.042 0.260 4144 Planarity : 0.005 0.067 4762 Dihedral : 5.921 82.403 3712 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.47 % Favored : 94.41 % Rotamer: Outliers : 4.61 % Allowed : 23.03 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3326 helix: 1.50 (0.14), residues: 1446 sheet: 0.57 (0.30), residues: 306 loop : -0.75 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 765 HIS 0.008 0.001 HIS A1807 PHE 0.032 0.002 PHE B2675 TYR 0.020 0.001 TYR B 401 ARG 0.011 0.000 ARG B2233 ********************** 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 745 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 608 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.7649 (mp10) cc_final: 0.7115 (mp10) REVERT: A 49 LYS cc_start: 0.8643 (tptt) cc_final: 0.8197 (mmmm) REVERT: A 75 GLN cc_start: 0.7942 (pm20) cc_final: 0.6606 (pp30) REVERT: A 361 GLN cc_start: 0.7978 (pt0) cc_final: 0.7700 (pt0) REVERT: A 392 GLN cc_start: 0.7468 (pp30) cc_final: 0.6887 (pt0) REVERT: A 426 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6953 (mm) REVERT: A 433 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6673 (ttm-80) REVERT: A 494 TRP cc_start: 0.7679 (p-90) cc_final: 0.7295 (p-90) REVERT: A 736 LYS cc_start: 0.7891 (ptmm) cc_final: 0.7415 (ptpp) REVERT: A 822 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8386 (mmp) REVERT: A 867 ILE cc_start: 0.8635 (mm) cc_final: 0.8346 (mm) REVERT: A 875 THR cc_start: 0.7828 (p) cc_final: 0.7546 (p) REVERT: A 889 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8008 (tmm-80) REVERT: A 894 ASN cc_start: 0.8505 (m110) cc_final: 0.8165 (m110) REVERT: A 1090 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7933 (tppp) REVERT: A 1139 ILE cc_start: 0.8583 (mt) cc_final: 0.8359 (mp) REVERT: A 1222 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7729 (mmmm) REVERT: A 1263 ASN cc_start: 0.7763 (p0) cc_final: 0.7476 (p0) REVERT: A 1314 MET cc_start: 0.6583 (ttp) cc_final: 0.6228 (ttp) REVERT: A 1488 MET cc_start: 0.8645 (ttp) cc_final: 0.8435 (ttm) REVERT: A 1511 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 1515 SER cc_start: 0.8120 (p) cc_final: 0.7725 (p) REVERT: A 1833 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: A 1881 ARG cc_start: 0.3075 (OUTLIER) cc_final: 0.2826 (mtt180) REVERT: A 1957 TRP cc_start: 0.8587 (t-100) cc_final: 0.8269 (t-100) REVERT: A 1959 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7979 (ttmm) REVERT: A 2024 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8062 (mtm110) REVERT: A 2052 ASP cc_start: 0.7772 (t70) cc_final: 0.7379 (t70) REVERT: A 2102 MET cc_start: 0.3296 (ppp) cc_final: 0.2887 (pp-130) REVERT: A 2176 MET cc_start: 0.5993 (tpt) cc_final: 0.5704 (tpt) REVERT: A 2178 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7150 (pmm) REVERT: A 2211 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8055 (pp) REVERT: A 2219 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7506 (mp0) REVERT: A 2237 SER cc_start: 0.6824 (OUTLIER) cc_final: 0.6061 (m) REVERT: A 2520 LYS cc_start: 0.7623 (mttt) cc_final: 0.7264 (mttt) REVERT: A 2544 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7469 (mm-30) REVERT: A 2575 MET cc_start: 0.8118 (tpp) cc_final: 0.7870 (tpt) REVERT: A 2630 ASN cc_start: 0.8241 (t0) cc_final: 0.7854 (t0) REVERT: A 2640 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: A 2689 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7209 (tpp) REVERT: A 2753 THR cc_start: 0.6673 (m) cc_final: 0.6222 (p) REVERT: A 2760 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.6466 (pm20) REVERT: A 2774 VAL cc_start: 0.8447 (m) cc_final: 0.8176 (p) REVERT: B 27 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7393 (tm-30) REVERT: B 28 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8234 (ttmm) REVERT: B 45 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: B 63 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7377 (mm-30) REVERT: B 417 LEU cc_start: 0.8408 (mt) cc_final: 0.8147 (mt) REVERT: B 501 GLN cc_start: 0.7795 (mt0) cc_final: 0.7461 (mt0) REVERT: B 505 MET cc_start: 0.6660 (mmm) cc_final: 0.6337 (mmm) REVERT: B 507 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7792 (mm-30) REVERT: B 834 ASP cc_start: 0.7542 (p0) cc_final: 0.7098 (p0) REVERT: B 885 TYR cc_start: 0.8532 (t80) cc_final: 0.8288 (t80) REVERT: B 1082 LYS cc_start: 0.7793 (pptt) cc_final: 0.7574 (pptt) REVERT: B 1096 VAL cc_start: 0.9248 (p) cc_final: 0.9011 (t) REVERT: B 1143 GLU cc_start: 0.6939 (tp30) cc_final: 0.6679 (tp30) REVERT: B 1263 ASN cc_start: 0.7878 (p0) cc_final: 0.7617 (p0) REVERT: B 1511 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7061 (tm-30) REVERT: B 1691 LEU cc_start: -0.0350 (OUTLIER) cc_final: -0.1193 (mt) REVERT: B 1825 VAL cc_start: 0.8506 (t) cc_final: 0.8154 (m) REVERT: B 1833 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: B 1959 LYS cc_start: 0.8310 (ttmm) cc_final: 0.8048 (ttmm) REVERT: B 2248 ARG cc_start: 0.7102 (mpp-170) cc_final: 0.6886 (mpp-170) REVERT: B 2301 GLN cc_start: 0.8436 (tt0) cc_final: 0.8168 (mt0) REVERT: B 2543 ASN cc_start: 0.8367 (t0) cc_final: 0.8149 (t0) REVERT: B 2562 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8193 (ttpp) REVERT: B 2563 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8628 (m) REVERT: B 2575 MET cc_start: 0.6885 (tpp) cc_final: 0.6565 (tpp) REVERT: B 2598 MET cc_start: 0.7374 (ptp) cc_final: 0.7027 (ppp) REVERT: B 2637 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7580 (mmmm) REVERT: B 2708 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6835 (mm) REVERT: B 2723 MET cc_start: 0.7252 (tpp) cc_final: 0.6497 (tpp) REVERT: B 2743 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7776 (mt-10) outliers start: 137 outliers final: 107 residues processed: 689 average time/residue: 1.3105 time to fit residues: 1065.8815 Evaluate side-chains 720 residues out of total 2974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 594 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 34 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 433 ARG 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 734 THR 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 818 THR 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 917 ASP Chi-restraints excluded: chain A residue 1118 MET Chi-restraints excluded: chain A residue 1164 ASN 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 1235 TRP Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1347 SER Chi-restraints excluded: chain A residue 1350 ASN Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1516 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 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 2024 ARG Chi-restraints excluded: chain A residue 2028 SER Chi-restraints excluded: chain A residue 2030 THR Chi-restraints excluded: chain A residue 2086 MET 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 2245 ASP Chi-restraints excluded: chain A residue 2249 ASP Chi-restraints excluded: chain A residue 2306 ASN Chi-restraints excluded: chain A residue 2539 CYS Chi-restraints excluded: chain A residue 2550 LEU Chi-restraints excluded: chain A residue 2618 ILE Chi-restraints excluded: chain A residue 2623 ASN Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2724 THR Chi-restraints excluded: chain A residue 2760 GLN 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 423 LYS Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 479 CYS 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 572 CYS Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 769 CYS Chi-restraints excluded: chain B residue 773 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 836 LEU Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 911 PHE Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1164 ASN Chi-restraints excluded: chain B residue 1195 GLU Chi-restraints excluded: chain B residue 1229 THR 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 1377 THR 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 1718 VAL Chi-restraints excluded: chain B residue 1789 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 1952 GLN Chi-restraints excluded: chain B residue 1955 ILE Chi-restraints excluded: chain B residue 2090 VAL Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2306 ASN Chi-restraints excluded: chain B residue 2539 CYS Chi-restraints excluded: chain B residue 2540 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 2627 THR Chi-restraints excluded: chain B residue 2649 GLN Chi-restraints excluded: chain B residue 2671 THR Chi-restraints excluded: chain B residue 2708 LEU Chi-restraints excluded: chain B residue 2722 SER Chi-restraints excluded: chain B residue 2749 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 0.0030 chunk 266 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN ** A 914 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1411 ASN A1720 ASN A1962 ASN ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 849 HIS ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 HIS B2236 GLN ** B2262 HIS ** 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 = 0.4191 r_free = 0.4191 target = 0.160412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134404 restraints weight = 42836.944| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.48 r_work: 0.3737 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27152 Z= 0.214 Angle : 0.645 12.683 36788 Z= 0.313 Chirality : 0.042 0.258 4144 Planarity : 0.005 0.066 4762 Dihedral : 5.860 82.150 3710 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.59 % Rotamer: Outliers : 4.67 % Allowed : 23.00 % Favored : 72.33 % 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: 0.57 (0.15), residues: 3326 helix: 1.53 (0.14), residues: 1434 sheet: 0.57 (0.30), residues: 296 loop : -0.73 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 765 HIS 0.008 0.001 HIS A1807 PHE 0.035 0.001 PHE A1087 TYR 0.029 0.001 TYR A2506 ARG 0.014 0.000 ARG A2676 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15668.34 seconds wall clock time: 275 minutes 15.85 seconds (16515.85 seconds total)