Starting phenix.real_space_refine on Fri Aug 9 07:55:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bja_16087/08_2024/8bja_16087.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bja_16087/08_2024/8bja_16087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bja_16087/08_2024/8bja_16087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bja_16087/08_2024/8bja_16087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bja_16087/08_2024/8bja_16087.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bja_16087/08_2024/8bja_16087.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 186 5.16 5 C 15984 2.51 5 N 4379 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B GLU 655": "OE1" <-> "OE2" Residue "B GLU 902": "OE1" <-> "OE2" Residue "B GLU 1143": "OE1" <-> "OE2" Residue "B GLU 2064": "OE1" <-> "OE2" Residue "B GLU 2202": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A GLU 1151": "OE1" <-> "OE2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "A GLU 1367": "OE1" <-> "OE2" Residue "A GLU 2046": "OE1" <-> "OE2" Residue "A GLU 2214": "OE1" <-> "OE2" Residue "A GLU 2284": "OE1" <-> "OE2" Residue "A GLU 2523": "OE1" <-> "OE2" Residue "A GLU 2640": "OE1" <-> "OE2" Residue "A GLU 2668": "OE1" <-> "OE2" Residue "A GLU 2673": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25204 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 12897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1638, 12897 Classifications: {'peptide': 1638} Link IDs: {'PCIS': 1, 'PTRANS': 88, 'TRANS': 1548} Chain breaks: 16 Chain: "A" Number of atoms: 12301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1563, 12301 Classifications: {'peptide': 1563} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 80, 'TRANS': 1481} Chain breaks: 14 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 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} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5253 SG CYS B1179 39.436 171.350 55.470 1.00 66.98 S ATOM 5478 SG CYS B1208 42.438 169.336 54.342 1.00 69.84 S ATOM 5500 SG CYS B1211 42.912 173.033 54.677 1.00 87.22 S ATOM 5663 SG CYS B1232 42.213 170.973 57.805 1.00 98.07 S ATOM 5500 SG CYS B1211 42.912 173.033 54.677 1.00 87.22 S ATOM 5529 SG CYS B1215 44.429 176.041 52.948 1.00 85.53 S ATOM 5677 SG CYS B1234 44.595 175.645 56.872 1.00 90.22 S ATOM 5730 SG CYS B1240 41.311 176.308 55.093 1.00 86.27 S ATOM 5393 SG CYS B1196 52.719 175.211 58.676 1.00 77.40 S ATOM 5417 SG CYS B1199 50.490 178.389 58.456 1.00 94.11 S ATOM 18033 SG CYS A1179 102.295 78.869 61.007 1.00 44.00 S ATOM 18258 SG CYS A1208 99.498 81.366 60.172 1.00 77.93 S ATOM 18280 SG CYS A1211 98.853 77.753 59.509 1.00 86.60 S ATOM 18443 SG CYS A1232 99.241 79.057 63.109 1.00 84.81 S ATOM 18280 SG CYS A1211 98.853 77.753 59.509 1.00 86.60 S ATOM 18309 SG CYS A1215 97.800 74.643 57.497 1.00 71.63 S ATOM 18457 SG CYS A1234 97.050 74.834 61.184 1.00 89.91 S ATOM 18510 SG CYS A1240 100.669 74.515 59.965 1.00 87.02 S ATOM 18173 SG CYS A1196 88.440 75.296 61.168 1.00 79.54 S ATOM 18197 SG CYS A1199 91.042 72.408 61.596 1.00102.08 S Residues with excluded nonbonded symmetry interactions: 241 residue: pdb=" N ILE B 528 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 528 " occ=0.00 residue: pdb=" N THR B 529 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 529 " occ=0.00 residue: pdb=" N VAL B 530 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 530 " occ=0.00 residue: pdb=" N GLY B 531 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 531 " occ=0.00 residue: pdb=" N THR B 532 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 532 " occ=0.00 residue: pdb=" N GLN B 533 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN B 533 " occ=0.00 residue: pdb=" N VAL B 534 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 534 " occ=0.00 residue: pdb=" N CYS B 535 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS B 535 " occ=0.00 residue: pdb=" N LEU B 536 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 536 " occ=0.00 residue: pdb=" N ARG B 537 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 537 " occ=0.00 residue: pdb=" N ASN B 538 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN B 538 " occ=0.00 residue: pdb=" N ASN B 539 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN B 539 " occ=0.00 ... (remaining 229 not shown) Time building chain proxies: 14.20, per 1000 atoms: 0.56 Number of scatterers: 25204 At special positions: 0 Unit cell: (141.455, 251.641, 129.543, 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 186 16.00 O 4649 8.00 N 4379 7.00 C 15984 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: 9.98 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2901 " pdb="ZN ZN A2901 " - pdb=" SG CYS A1232 " pdb="ZN ZN A2901 " - pdb=" SG CYS A1208 " pdb="ZN ZN A2901 " - pdb=" SG CYS A1179 " pdb="ZN ZN A2901 " - pdb=" SG CYS A1211 " pdb=" ZN A2902 " pdb="ZN ZN A2902 " - pdb=" SG CYS A1234 " pdb="ZN ZN A2902 " - pdb=" SG CYS A1240 " pdb="ZN ZN A2902 " - pdb=" SG CYS A1211 " pdb="ZN ZN A2902 " - pdb=" SG CYS A1215 " pdb=" ZN A2903 " pdb="ZN ZN A2903 " - pdb=" ND1 HIS A1219 " pdb="ZN ZN A2903 " - pdb=" ND1 HIS A1216 " pdb="ZN ZN A2903 " - pdb=" SG CYS A1196 " pdb="ZN ZN A2903 " - pdb=" SG CYS A1199 " pdb=" ZN B2901 " pdb="ZN ZN B2901 " - pdb=" SG CYS B1179 " pdb="ZN ZN B2901 " - pdb=" SG CYS B1232 " pdb="ZN ZN B2901 " - pdb=" SG CYS B1208 " pdb="ZN ZN B2901 " - pdb=" SG CYS B1211 " pdb=" ZN B2902 " pdb="ZN ZN B2902 " - pdb=" SG CYS B1240 " pdb="ZN ZN B2902 " - pdb=" SG CYS B1211 " pdb="ZN ZN B2902 " - pdb=" SG CYS B1234 " pdb="ZN ZN B2902 " - pdb=" SG CYS B1215 " pdb=" ZN B2903 " pdb="ZN ZN B2903 " - pdb=" NE2 HIS B1216 " pdb="ZN ZN B2903 " - pdb=" ND1 HIS B1219 " pdb="ZN ZN B2903 " - pdb=" SG CYS B1196 " pdb="ZN ZN B2903 " - pdb=" SG CYS B1199 " Number of angles added : 27 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6082 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 32 sheets defined 47.6% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'B' and resid 14 through 32 removed outlier: 3.584A pdb=" N LEU B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 45 removed outlier: 4.100A pdb=" N GLN B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 removed outlier: 5.201A pdb=" N SER B 453 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 515 removed outlier: 4.303A pdb=" N LYS B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 removed outlier: 4.142A pdb=" N LYS B 583 " --> pdb=" O PRO B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.534A pdb=" N ASP B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 793 removed outlier: 3.608A pdb=" N GLY B 793 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 799 removed outlier: 3.533A pdb=" N ASN B 798 " --> pdb=" O ASN B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 882 removed outlier: 3.643A pdb=" N LEU B 881 " --> pdb=" O MET B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 900 removed outlier: 3.617A pdb=" N LEU B 892 " --> pdb=" O CYS B 888 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET B 893 " --> pdb=" O ARG B 889 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN B 894 " --> pdb=" O GLN B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.750A pdb=" N SER B 913 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 929 Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 3.571A pdb=" N ALA B1083 " --> pdb=" O LYS B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1116 through 1123 Processing helix chain 'B' and resid 1125 through 1142 removed outlier: 3.545A pdb=" N ALA B1142 " --> pdb=" O LYS B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1147 Processing helix chain 'B' and resid 1149 through 1156 removed outlier: 3.933A pdb=" N VAL B1153 " --> pdb=" O LYS B1149 " (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 1233 through 1238 removed outlier: 4.238A pdb=" N LYS B1237 " --> pdb=" O ASP B1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1259 Processing helix chain 'B' and resid 1274 through 1290 removed outlier: 4.099A pdb=" N VAL B1288 " --> pdb=" O ALA B1284 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B1290 " --> pdb=" O GLN B1286 " (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 1324 through 1334 removed outlier: 3.640A pdb=" N GLN B1334 " --> pdb=" O GLU B1330 " (cutoff:3.500A) Processing helix chain 'B' and resid 1335 through 1344 Processing helix chain 'B' and resid 1358 through 1362 Processing helix chain 'B' and resid 1365 through 1372 Processing helix chain 'B' and resid 1377 through 1389 Processing helix chain 'B' and resid 1396 through 1409 Processing helix chain 'B' and resid 1416 through 1443 removed outlier: 3.572A pdb=" N GLU B1420 " --> pdb=" O GLY B1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 1454 through 1467 Processing helix chain 'B' and resid 1467 through 1488 removed outlier: 3.525A pdb=" N GLU B1473 " --> pdb=" O PRO B1469 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN B1477 " --> pdb=" O GLU B1473 " (cutoff:3.500A) Proline residue: B1485 - end of helix removed outlier: 3.827A pdb=" N MET B1488 " --> pdb=" O VAL B1484 " (cutoff:3.500A) Processing helix chain 'B' and resid 1502 through 1515 removed outlier: 3.717A pdb=" N ALA B1506 " --> pdb=" O THR B1502 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B1511 " --> pdb=" O MET B1507 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B1512 " --> pdb=" O GLN B1508 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B1513 " --> pdb=" O GLY B1509 " (cutoff:3.500A) Processing helix chain 'B' and resid 1777 through 1800 Processing helix chain 'B' and resid 1804 through 1809 Processing helix chain 'B' and resid 1820 through 1860 Proline residue: B1837 - end of helix removed outlier: 3.622A pdb=" N ILE B1845 " --> pdb=" O TRP B1841 " (cutoff:3.500A) Processing helix chain 'B' and resid 1912 through 1929 removed outlier: 4.340A pdb=" N ASN B1929 " --> pdb=" O MET B1925 " (cutoff:3.500A) Processing helix chain 'B' and resid 1940 through 1943 removed outlier: 3.571A pdb=" N SER B1943 " --> pdb=" O ASP B1940 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1940 through 1943' Processing helix chain 'B' and resid 1944 through 1964 Processing helix chain 'B' and resid 2044 through 2048 Processing helix chain 'B' and resid 2048 through 2053 removed outlier: 3.679A pdb=" N ASP B2052 " --> pdb=" O ILE B2048 " (cutoff:3.500A) Processing helix chain 'B' and resid 2062 through 2066 Processing helix chain 'B' and resid 2103 through 2114 Processing helix chain 'B' and resid 2165 through 2169 Processing helix chain 'B' and resid 2181 through 2189 Processing helix chain 'B' and resid 2190 through 2200 Processing helix chain 'B' and resid 2203 through 2207 removed outlier: 3.697A pdb=" N ALA B2206 " --> pdb=" O ASP B2203 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B2207 " --> pdb=" O VAL B2204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2203 through 2207' Processing helix chain 'B' and resid 2217 through 2236 removed outlier: 4.239A pdb=" N SER B2223 " --> pdb=" O GLU B2219 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B2224 " --> pdb=" O VAL B2220 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B2225 " --> pdb=" O LYS B2221 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B2226 " --> pdb=" O GLU B2222 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B2236 " --> pdb=" O LEU B2232 " (cutoff:3.500A) Processing helix chain 'B' and resid 2247 through 2267 removed outlier: 3.742A pdb=" N LEU B2259 " --> pdb=" O THR B2255 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B2260 " --> pdb=" O MET B2256 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B2265 " --> pdb=" O ASN B2261 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B2266 " --> pdb=" O HIS B2262 " (cutoff:3.500A) Processing helix chain 'B' and resid 2288 through 2305 Processing helix chain 'B' and resid 2522 through 2540 removed outlier: 3.651A pdb=" N ASN B2527 " --> pdb=" O GLU B2523 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B2528 " --> pdb=" O ALA B2524 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B2535 " --> pdb=" O ASN B2531 " (cutoff:3.500A) Processing helix chain 'B' and resid 2551 through 2559 removed outlier: 4.239A pdb=" N VAL B2557 " --> pdb=" O HIS B2553 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B2558 " --> pdb=" O VAL B2554 " (cutoff:3.500A) Processing helix chain 'B' and resid 2564 through 2571 removed outlier: 3.539A pdb=" N PHE B2568 " --> pdb=" O TRP B2565 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B2569 " --> pdb=" O HIS B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2586 removed outlier: 3.844A pdb=" N SER B2578 " --> pdb=" O VAL B2574 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B2579 " --> pdb=" O MET B2575 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B2580 " --> pdb=" O TYR B2576 " (cutoff:3.500A) Processing helix chain 'B' and resid 2587 through 2589 No H-bonds generated for 'chain 'B' and resid 2587 through 2589' Processing helix chain 'B' and resid 2590 through 2599 removed outlier: 3.693A pdb=" N ALA B2597 " --> pdb=" O ALA B2593 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET B2598 " --> pdb=" O VAL B2594 " (cutoff:3.500A) Processing helix chain 'B' and resid 2627 through 2630 Processing helix chain 'B' and resid 2631 through 2644 Processing helix chain 'B' and resid 2647 through 2662 removed outlier: 3.771A pdb=" N LYS B2656 " --> pdb=" O HIS B2652 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B2661 " --> pdb=" O GLY B2657 " (cutoff:3.500A) Processing helix chain 'B' and resid 2663 through 2667 removed outlier: 3.503A pdb=" N LEU B2667 " --> pdb=" O LYS B2664 " (cutoff:3.500A) Processing helix chain 'B' and resid 2671 through 2680 removed outlier: 3.577A pdb=" N ASN B2680 " --> pdb=" O ARG B2676 " (cutoff:3.500A) Processing helix chain 'B' and resid 2686 through 2693 removed outlier: 3.553A pdb=" N LEU B2690 " --> pdb=" O ASN B2686 " (cutoff:3.500A) Processing helix chain 'B' and resid 2703 through 2719 removed outlier: 3.884A pdb=" N GLU B2719 " --> pdb=" O TRP B2715 " (cutoff:3.500A) Processing helix chain 'B' and resid 2722 through 2735 removed outlier: 3.677A pdb=" N ARG B2726 " --> pdb=" O SER B2722 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B2727 " --> pdb=" O MET B2723 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP B2728 " --> pdb=" O THR B2724 " (cutoff:3.500A) Processing helix chain 'B' and resid 2779 through 2794 removed outlier: 3.556A pdb=" N LEU B2783 " --> pdb=" O SER B2779 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 32 removed outlier: 3.573A pdb=" N GLU A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 removed outlier: 4.311A pdb=" N SER A 453 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 4.107A pdb=" N GLY A 470 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 515 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 874 through 882 removed outlier: 3.536A pdb=" N HIS A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 881 " --> pdb=" O MET A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 900 removed outlier: 3.510A pdb=" N GLN A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 892 " --> pdb=" O CYS A 888 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET A 893 " --> pdb=" O ARG A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 906 removed outlier: 4.224A pdb=" N LEU A 905 " --> pdb=" O GLU A 902 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 906 " --> pdb=" O GLN A 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 902 through 906' Processing helix chain 'A' and resid 907 through 913 removed outlier: 3.580A pdb=" N SER A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 930 removed outlier: 3.548A pdb=" N CYS A 926 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS A 930 " --> pdb=" O CYS A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1094 removed outlier: 4.165A pdb=" N HIS A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A1087 " --> pdb=" O ALA A1083 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1107 removed outlier: 3.548A pdb=" N LEU A1105 " --> pdb=" O TYR A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1125 through 1141 removed outlier: 3.669A pdb=" N THR A1131 " --> pdb=" O PRO A1127 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A1141 " --> pdb=" O GLN A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1156 removed outlier: 3.775A pdb=" N PHE A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1167 Processing helix chain 'A' and resid 1168 through 1175 Processing helix chain 'A' and resid 1180 through 1185 Processing helix chain 'A' and resid 1209 through 1213 removed outlier: 3.938A pdb=" N ARG A1213 " --> pdb=" O THR A1209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1209 through 1213' Processing helix chain 'A' and resid 1233 through 1238 removed outlier: 3.897A pdb=" N LYS A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1262 Processing helix chain 'A' and resid 1274 through 1290 removed outlier: 3.797A pdb=" N VAL A1288 " --> pdb=" O ALA A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1293 No H-bonds generated for 'chain 'A' and resid 1291 through 1293' Processing helix chain 'A' and resid 1325 through 1333 Processing helix chain 'A' and resid 1335 through 1344 removed outlier: 3.735A pdb=" N LEU A1339 " --> pdb=" O ASP A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1369 Processing helix chain 'A' and resid 1377 through 1389 Processing helix chain 'A' and resid 1395 through 1410 Processing helix chain 'A' and resid 1417 through 1443 Processing helix chain 'A' and resid 1454 through 1467 Processing helix chain 'A' and resid 1467 through 1488 removed outlier: 4.187A pdb=" N GLU A1473 " --> pdb=" O PRO A1469 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A1474 " --> pdb=" O TYR A1470 " (cutoff:3.500A) Proline residue: A1485 - end of helix Processing helix chain 'A' and resid 1502 through 1514 removed outlier: 3.527A pdb=" N GLU A1512 " --> pdb=" O GLN A1508 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1513 " --> pdb=" O GLY A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1801 removed outlier: 3.548A pdb=" N GLN A1794 " --> pdb=" O ILE A1790 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A1801 " --> pdb=" O ASP A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1809 Processing helix chain 'A' and resid 1821 through 1863 removed outlier: 3.502A pdb=" N VAL A1825 " --> pdb=" O TYR A1821 " (cutoff:3.500A) Proline residue: A1837 - end of helix Processing helix chain 'A' and resid 1912 through 1929 removed outlier: 3.550A pdb=" N ASN A1919 " --> pdb=" O GLY A1915 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A1920 " --> pdb=" O ASP A1916 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1940 through 1943 Processing helix chain 'A' and resid 1944 through 1962 removed outlier: 3.676A pdb=" N VAL A1950 " --> pdb=" O HIS A1946 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A1962 " --> pdb=" O ILE A1958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2048 removed outlier: 3.617A pdb=" N ILE A2048 " --> pdb=" O LEU A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2048 through 2053 removed outlier: 3.815A pdb=" N ASP A2052 " --> pdb=" O ILE A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2062 through 2067 removed outlier: 3.591A pdb=" N LEU A2066 " --> pdb=" O ARG A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2183 through 2189 Processing helix chain 'A' and resid 2189 through 2196 Processing helix chain 'A' and resid 2210 through 2216 removed outlier: 3.632A pdb=" N GLU A2214 " --> pdb=" O SER A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2217 through 2236 removed outlier: 3.987A pdb=" N SER A2223 " --> pdb=" O GLU A2219 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A2232 " --> pdb=" O GLU A2228 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A2236 " --> pdb=" O LEU A2232 " (cutoff:3.500A) Processing helix chain 'A' and resid 2247 through 2266 removed outlier: 3.504A pdb=" N ILE A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A2261 " --> pdb=" O ARG A2257 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A2265 " --> pdb=" O ASN A2261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A2266 " --> pdb=" O HIS A2262 " (cutoff:3.500A) Processing helix chain 'A' and resid 2288 through 2305 removed outlier: 3.521A pdb=" N ALA A2292 " --> pdb=" O GLY A2288 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A2302 " --> pdb=" O ALA A2298 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A2303 " --> pdb=" O ILE A2299 " (cutoff:3.500A) Processing helix chain 'A' and resid 2522 through 2543 removed outlier: 3.608A pdb=" N GLY A2533 " --> pdb=" O PHE A2529 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A2534 " --> pdb=" O ARG A2530 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A2535 " --> pdb=" O ASN A2531 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A2536 " --> pdb=" O ILE A2532 " (cutoff:3.500A) Processing helix chain 'A' and resid 2551 through 2560 Processing helix chain 'A' and resid 2567 through 2572 removed outlier: 3.592A pdb=" N PHE A2571 " --> pdb=" O ASP A2567 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A2572 " --> pdb=" O PHE A2568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2567 through 2572' Processing helix chain 'A' and resid 2572 through 2586 removed outlier: 4.280A pdb=" N TYR A2576 " --> pdb=" O ASP A2572 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A2582 " --> pdb=" O SER A2578 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A2583 " --> pdb=" O LEU A2579 " (cutoff:3.500A) Processing helix chain 'A' and resid 2587 through 2589 No H-bonds generated for 'chain 'A' and resid 2587 through 2589' Processing helix chain 'A' and resid 2590 through 2599 Processing helix chain 'A' and resid 2630 through 2644 removed outlier: 4.290A pdb=" N ARG A2636 " --> pdb=" O TYR A2632 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A2637 " --> pdb=" O GLU A2633 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A2640 " --> pdb=" O ARG A2636 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A2641 " --> pdb=" O LYS A2637 " (cutoff:3.500A) Processing helix chain 'A' and resid 2647 through 2660 removed outlier: 4.427A pdb=" N LYS A2656 " --> pdb=" O HIS A2652 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A2657 " --> pdb=" O ALA A2653 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A2658 " --> pdb=" O MET A2654 " (cutoff:3.500A) Processing helix chain 'A' and resid 2663 through 2667 removed outlier: 3.575A pdb=" N SER A2666 " --> pdb=" O PRO A2663 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A2667 " --> pdb=" O LYS A2664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2663 through 2667' Processing helix chain 'A' and resid 2671 through 2681 removed outlier: 3.543A pdb=" N ARG A2676 " --> pdb=" O ALA A2672 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A2677 " --> pdb=" O GLU A2673 " (cutoff:3.500A) Processing helix chain 'A' and resid 2686 through 2694 removed outlier: 3.941A pdb=" N SER A2692 " --> pdb=" O GLN A2688 " (cutoff:3.500A) Processing helix chain 'A' and resid 2710 through 2721 Processing helix chain 'A' and resid 2722 through 2724 No H-bonds generated for 'chain 'A' and resid 2722 through 2724' Processing helix chain 'A' and resid 2725 through 2735 Processing helix chain 'A' and resid 2742 through 2746 removed outlier: 3.666A pdb=" N PHE A2746 " --> pdb=" O GLU A2743 " (cutoff:3.500A) Processing helix chain 'A' and resid 2780 through 2794 removed outlier: 3.916A pdb=" N GLN A2785 " --> pdb=" O GLN A2781 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A2786 " --> pdb=" O ILE A2782 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A2793 " --> pdb=" O LEU A2789 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS A2794 " --> pdb=" O ALA A2790 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 11 removed outlier: 4.161A pdb=" N LYS B 863 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 53 removed outlier: 4.043A pdb=" N GLN B 50 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 53 removed outlier: 4.043A pdb=" N GLN B 50 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 69 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 361 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 371 through 374 removed outlier: 7.040A pdb=" N VAL B 384 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 424 through 429 removed outlier: 6.954A pdb=" N ALA B 437 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 427 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR B 435 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA B 429 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL B 443 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 462 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 445 " --> pdb=" O HIS B 460 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.818A pdb=" N SER B 475 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 709 through 712 removed outlier: 3.855A pdb=" N LYS B 672 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS B 681 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 670 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 648 through 652 removed outlier: 3.665A pdb=" N GLU B 649 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 657 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 745 through 752 removed outlier: 5.816A pdb=" N ILE B 746 " --> pdb=" O LYS B 761 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS B 761 " --> pdb=" O ILE B 746 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 748 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 755 " --> pdb=" O ASP B 752 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 745 through 752 removed outlier: 5.816A pdb=" N ILE B 746 " --> pdb=" O LYS B 761 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS B 761 " --> pdb=" O ILE B 746 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 748 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 755 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE B 770 " --> pdb=" O GLU B 779 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 801 through 803 removed outlier: 4.756A pdb=" N LEU B 812 " --> pdb=" O TYR B 820 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1189 through 1190 Processing sheet with id=AB4, first strand: chain 'B' and resid 1193 through 1196 removed outlier: 4.613A pdb=" N ILE B1193 " --> pdb=" O LYS B1224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 2240 through 2244 Processing sheet with id=AB6, first strand: chain 'B' and resid 2505 through 2506 removed outlier: 3.985A pdb=" N THR B2515 " --> pdb=" O TYR B2506 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 2603 through 2605 Processing sheet with id=AB8, first strand: chain 'B' and resid 2695 through 2698 removed outlier: 3.704A pdb=" N ILE B2754 " --> pdb=" O ASN B2697 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2 through 9 removed outlier: 4.069A pdb=" N SER A 843 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU A 872 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 841 " --> pdb=" O GLU A 872 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 48 through 53 Processing sheet with id=AC2, first strand: chain 'A' and resid 371 through 374 removed outlier: 6.848A pdb=" N VAL A 384 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 424 through 429 removed outlier: 3.767A pdb=" N LEU A 426 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 443 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA A 462 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AC5, first strand: chain 'A' and resid 708 through 712 removed outlier: 7.247A pdb=" N TYR A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL A 673 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA A 679 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.631A pdb=" N PHE A 549 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE A 658 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ILE A 551 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 656 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 745 through 752 removed outlier: 6.590A pdb=" N VAL A 759 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 749 " --> pdb=" O HIS A 757 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N HIS A 757 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL A 751 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 760 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 782 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 770 " --> pdb=" O GLN A 780 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN A 780 " --> pdb=" O ILE A 770 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.426A pdb=" N LEU A 812 " --> pdb=" O TYR A 820 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1189 through 1190 Processing sheet with id=AD1, first strand: chain 'A' and resid 1207 through 1208 removed outlier: 4.831A pdb=" N ILE A1193 " --> pdb=" O LYS A1224 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 2240 through 2244 removed outlier: 3.807A pdb=" N THR A2280 " --> pdb=" O LEU A2242 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A2244 " --> pdb=" O THR A2280 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 2505 through 2506 Processing sheet with id=AD4, first strand: chain 'A' and resid 2603 through 2605 Processing sheet with id=AD5, first strand: chain 'A' and resid 2751 through 2755 1050 hydrogen bonds defined for protein. 3006 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: 11.14 Time building geometry restraints manager: 11.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7975 1.34 - 1.46: 3902 1.46 - 1.58: 13556 1.58 - 1.70: 0 1.70 - 1.82: 272 Bond restraints: 25705 Sorted by residual: bond pdb=" N VAL B1097 " pdb=" CA VAL B1097 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.19e-02 7.06e+03 9.55e+00 bond pdb=" N ILE B2252 " pdb=" CA ILE B2252 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.82e+00 bond pdb=" N ILE B2535 " pdb=" CA ILE B2535 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.57e+00 bond pdb=" N ASP B2247 " pdb=" CA ASP B2247 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.24e-02 6.50e+03 7.31e+00 bond pdb=" N GLN B2253 " pdb=" CA GLN B2253 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.97e+00 ... (remaining 25700 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.27: 558 105.27 - 112.50: 13162 112.50 - 119.72: 8762 119.72 - 126.94: 12004 126.94 - 134.16: 328 Bond angle restraints: 34814 Sorted by residual: angle pdb=" N VAL A1369 " pdb=" CA VAL A1369 " pdb=" C VAL A1369 " ideal model delta sigma weight residual 110.21 104.01 6.20 1.13e+00 7.83e-01 3.01e+01 angle pdb=" N LEU B2212 " pdb=" CA LEU B2212 " pdb=" C LEU B2212 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" CB MET A1342 " pdb=" CG MET A1342 " pdb=" SD MET A1342 " ideal model delta sigma weight residual 112.70 126.56 -13.86 3.00e+00 1.11e-01 2.13e+01 angle pdb=" CA GLN B2649 " pdb=" CB GLN B2649 " pdb=" CG GLN B2649 " ideal model delta sigma weight residual 114.10 122.86 -8.76 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CB MET A 1 " pdb=" CG MET A 1 " pdb=" SD MET A 1 " ideal model delta sigma weight residual 112.70 125.12 -12.42 3.00e+00 1.11e-01 1.71e+01 ... (remaining 34809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 13461 17.76 - 35.51: 1656 35.51 - 53.27: 458 53.27 - 71.03: 84 71.03 - 88.78: 31 Dihedral angle restraints: 15690 sinusoidal: 6354 harmonic: 9336 Sorted by residual: dihedral pdb=" CD ARG A2266 " pdb=" NE ARG A2266 " pdb=" CZ ARG A2266 " pdb=" NH1 ARG A2266 " ideal model delta sinusoidal sigma weight residual 0.00 53.90 -53.90 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA PRO A2036 " pdb=" C PRO A2036 " pdb=" N PRO A2037 " pdb=" CA PRO A2037 " ideal model delta harmonic sigma weight residual 180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASP A2203 " pdb=" C ASP A2203 " pdb=" N VAL A2204 " pdb=" CA VAL A2204 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 15687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2736 0.039 - 0.077: 892 0.077 - 0.116: 257 0.116 - 0.154: 61 0.154 - 0.193: 10 Chirality restraints: 3956 Sorted by residual: chirality pdb=" CA LEU B2251 " pdb=" N LEU B2251 " pdb=" C LEU B2251 " pdb=" CB LEU B2251 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CA ILE B2252 " pdb=" N ILE B2252 " pdb=" C ILE B2252 " pdb=" CB ILE B2252 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CB VAL A 497 " pdb=" CA VAL A 497 " pdb=" CG1 VAL A 497 " pdb=" CG2 VAL A 497 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 3953 not shown) Planarity restraints: 4473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2266 " -0.885 9.50e-02 1.11e+02 3.97e-01 9.54e+01 pdb=" NE ARG A2266 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG A2266 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A2266 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A2266 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B2248 " 0.429 9.50e-02 1.11e+02 1.92e-01 2.26e+01 pdb=" NE ARG B2248 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B2248 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B2248 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B2248 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B2246 " -0.412 9.50e-02 1.11e+02 1.85e-01 2.09e+01 pdb=" NE ARG B2246 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B2246 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B2246 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B2246 " -0.013 2.00e-02 2.50e+03 ... (remaining 4470 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1128 2.72 - 3.26: 26503 3.26 - 3.81: 40667 3.81 - 4.35: 49619 4.35 - 4.90: 81949 Nonbonded interactions: 199866 Sorted by model distance: nonbonded pdb=" O GLN A2542 " pdb=" ND2 ASN A2543 " model vdw 2.169 3.120 nonbonded pdb=" N GLN A1326 " pdb=" OE1 GLN A1326 " model vdw 2.183 3.120 nonbonded pdb=" OD1 ASP A 752 " pdb=" N SER A 753 " model vdw 2.189 3.120 nonbonded pdb=" OG SER B2289 " pdb=" O CYS B2768 " model vdw 2.208 3.040 nonbonded pdb=" O PRO B2099 " pdb=" OH TYR A1370 " model vdw 2.214 3.040 ... (remaining 199861 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 32 or resid 37 through 74 or resid 354 through 1 \ 108 or resid 1110 through 1113 or resid 1115 through 1293 or resid 1295 through \ 1874 or resid 1911 through 1930 or resid 1936 through 1965 or resid 2043 through \ 2797 or resid 2901 through 2903)) selection = (chain 'B' and (resid 1 through 515 or resid 530 through 577 or resid 650 throug \ h 684 or resid 703 through 938 or resid 1077 through 1293 or resid 1315 or resid \ 1324 through 1445 or resid 1453 through 1488 or resid 1495 through 1515 or resi \ d 1776 through 1930 or (resid 1936 and (name N or name CA or name C or name O or \ name CB )) or resid 1937 through 1938 or (resid 1939 and (name N or name CA or \ name C or name O or name CB )) or resid 1940 through 2067 or resid 2182 through \ 2696 or resid 2709 through 2797 or resid 2901 through 2903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 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: 1.800 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: 0.030 Extract box with map and model: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 75.500 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 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 0.051 25705 Z= 0.260 Angle : 0.808 13.855 34814 Z= 0.414 Chirality : 0.043 0.193 3956 Planarity : 0.009 0.397 4473 Dihedral : 17.120 88.782 9608 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.36 % Favored : 94.42 % Rotamer: Outliers : 3.67 % Allowed : 30.10 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.80 (0.15), residues: 3137 helix: -0.17 (0.14), residues: 1270 sheet: -0.15 (0.29), residues: 325 loop : -0.84 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 765 HIS 0.007 0.001 HIS B2182 PHE 0.015 0.001 PHE B2175 TYR 0.020 0.001 TYR A 465 ARG 0.022 0.001 ARG B 767 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 467 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 549 PHE cc_start: 0.0147 (p90) cc_final: -0.0057 (p90) REVERT: B 585 MET cc_start: 0.0018 (mtm) cc_final: -0.0509 (mtm) REVERT: B 731 PHE cc_start: 0.1846 (m-80) cc_final: 0.1344 (m-80) REVERT: B 780 GLN cc_start: 0.7076 (pm20) cc_final: 0.6631 (pm20) REVERT: B 795 ASN cc_start: 0.7344 (t0) cc_final: 0.7118 (t0) REVERT: B 873 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7431 (tmmm) REVERT: B 914 HIS cc_start: 0.7823 (p90) cc_final: 0.7144 (p-80) REVERT: B 1099 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 1152 ASP cc_start: 0.8143 (p0) cc_final: 0.7897 (p0) REVERT: B 2064 GLU cc_start: 0.6199 (tp30) cc_final: 0.5938 (tp30) REVERT: B 2198 ARG cc_start: 0.7609 (ttt180) cc_final: 0.7212 (ttp-170) REVERT: B 2218 PHE cc_start: 0.8431 (t80) cc_final: 0.8085 (t80) REVERT: B 2550 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5585 (mt) REVERT: B 2598 MET cc_start: 0.3976 (ppp) cc_final: 0.3266 (pmm) REVERT: B 2652 HIS cc_start: 0.7792 (t-90) cc_final: 0.7525 (t-90) REVERT: B 2728 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7263 (t0) REVERT: B 2736 SER cc_start: 0.7404 (t) cc_final: 0.6586 (p) REVERT: A 20 ASP cc_start: 0.7963 (m-30) cc_final: 0.7683 (m-30) REVERT: A 27 GLU cc_start: 0.7917 (pp20) cc_final: 0.7643 (pp20) REVERT: A 367 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6578 (p0) REVERT: A 372 ILE cc_start: 0.8309 (pt) cc_final: 0.7847 (mp) REVERT: A 377 LEU cc_start: 0.7161 (mm) cc_final: 0.6860 (mt) REVERT: A 475 SER cc_start: 0.8773 (t) cc_final: 0.8467 (p) REVERT: A 807 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6751 (tm-30) REVERT: A 838 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8769 (pp) REVERT: A 872 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7095 (mp0) REVERT: A 913 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.7919 (p) REVERT: A 915 ARG cc_start: 0.8039 (tpp-160) cc_final: 0.7811 (mmt180) REVERT: A 1192 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7907 (p0) REVERT: A 1359 ARG cc_start: 0.5172 (mtt180) cc_final: 0.3618 (mtt180) REVERT: A 1810 TYR cc_start: 0.8948 (t80) cc_final: 0.8699 (t80) REVERT: A 2052 ASP cc_start: 0.8076 (t0) cc_final: 0.7775 (OUTLIER) REVERT: A 2224 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8217 (tmmt) REVERT: A 2225 PHE cc_start: 0.8084 (t80) cc_final: 0.7779 (t80) REVERT: A 2262 HIS cc_start: 0.3637 (t70) cc_final: 0.3291 (t-90) REVERT: A 2544 GLU cc_start: 0.6710 (mp0) cc_final: 0.6233 (mp0) REVERT: A 2546 CYS cc_start: 0.7128 (t) cc_final: 0.6857 (p) REVERT: A 2598 MET cc_start: 0.6460 (mtt) cc_final: 0.6125 (mtt) REVERT: A 2726 ARG cc_start: 0.7085 (mtt-85) cc_final: 0.6741 (mtt90) outliers start: 103 outliers final: 61 residues processed: 557 average time/residue: 1.2846 time to fit residues: 830.8563 Evaluate side-chains 482 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 415 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 849 HIS Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1229 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1354 LEU Chi-restraints excluded: chain B residue 1355 SER Chi-restraints excluded: chain B residue 1382 CYS Chi-restraints excluded: chain B residue 1392 THR Chi-restraints excluded: chain B residue 1404 THR Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1861 SER Chi-restraints excluded: chain B residue 2167 THR Chi-restraints excluded: chain B residue 2172 GLN Chi-restraints excluded: chain B residue 2294 SER Chi-restraints excluded: chain B residue 2529 PHE Chi-restraints excluded: chain B residue 2541 LEU Chi-restraints excluded: chain B residue 2550 LEU Chi-restraints excluded: chain B residue 2728 ASP Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1355 SER Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1411 ASN Chi-restraints excluded: chain A residue 1431 SER Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1819 LEU Chi-restraints excluded: chain A residue 1820 THR Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 2239 ASP Chi-restraints excluded: chain A residue 2280 THR Chi-restraints excluded: chain A residue 2543 ASN Chi-restraints excluded: chain A residue 2584 LEU Chi-restraints excluded: chain A residue 2709 GLN Chi-restraints excluded: chain A residue 2738 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 0.9990 chunk 241 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 250 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN B2258 GLN B2301 GLN ** B2553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2649 GLN A 5 HIS A 30 ASN A1372 ASN A1870 HIS A1962 ASN ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 HIS A2507 GLN A2680 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25705 Z= 0.249 Angle : 0.744 10.966 34814 Z= 0.375 Chirality : 0.044 0.177 3956 Planarity : 0.006 0.061 4473 Dihedral : 7.101 126.065 3530 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.23 % Favored : 94.61 % Rotamer: Outliers : 4.85 % Allowed : 25.96 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.49 (0.15), residues: 3137 helix: 0.26 (0.14), residues: 1336 sheet: -0.05 (0.29), residues: 313 loop : -0.85 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 765 HIS 0.008 0.001 HIS A2262 PHE 0.027 0.002 PHE A2295 TYR 0.021 0.002 TYR A 891 ARG 0.025 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 423 time to evaluate : 2.709 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: B 765 TRP cc_start: 0.7665 (t60) cc_final: 0.6764 (t60) REVERT: B 780 GLN cc_start: 0.7129 (pm20) cc_final: 0.6772 (pm20) REVERT: B 795 ASN cc_start: 0.7309 (t0) cc_final: 0.6934 (t0) REVERT: B 868 ILE cc_start: 0.8170 (mm) cc_final: 0.7914 (pp) REVERT: B 890 GLN cc_start: 0.7388 (tp40) cc_final: 0.6955 (tp40) REVERT: B 914 HIS cc_start: 0.7859 (p90) cc_final: 0.7205 (p-80) REVERT: B 1084 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.7046 (m110) REVERT: B 1152 ASP cc_start: 0.8080 (p0) cc_final: 0.7872 (p0) REVERT: B 1238 CYS cc_start: 0.7964 (t) cc_final: 0.7751 (t) REVERT: B 1316 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7430 (p0) REVERT: B 1362 HIS cc_start: 0.5714 (OUTLIER) cc_final: 0.5225 (t70) REVERT: B 1399 ASP cc_start: 0.7746 (m-30) cc_final: 0.7479 (m-30) REVERT: B 1508 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7338 (tp-100) REVERT: B 1512 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7510 (mt-10) REVERT: B 1778 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8438 (mt) REVERT: B 1961 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7632 (tpp) REVERT: B 2184 MET cc_start: 0.8418 (tpt) cc_final: 0.8018 (tmm) REVERT: B 2198 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6759 (ttp-170) REVERT: B 2256 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6376 (mmm) REVERT: B 2301 GLN cc_start: 0.7955 (tp40) cc_final: 0.7723 (tp-100) REVERT: B 2506 TYR cc_start: 0.7874 (p90) cc_final: 0.7586 (p90) REVERT: B 2522 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7095 (p) REVERT: B 2562 LYS cc_start: 0.7907 (tppt) cc_final: 0.7680 (tmmt) REVERT: B 2600 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6233 (mt) REVERT: B 2671 THR cc_start: 0.7921 (p) cc_final: 0.7630 (t) REVERT: B 2736 SER cc_start: 0.7821 (t) cc_final: 0.7143 (p) REVERT: A 20 ASP cc_start: 0.7985 (m-30) cc_final: 0.7592 (m-30) REVERT: A 27 GLU cc_start: 0.7674 (pp20) cc_final: 0.7342 (pp20) REVERT: A 28 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7887 (tmtt) REVERT: A 37 HIS cc_start: 0.6583 (OUTLIER) cc_final: 0.5254 (t-90) REVERT: A 69 ARG cc_start: 0.6996 (tpt170) cc_final: 0.6788 (tpt170) REVERT: A 372 ILE cc_start: 0.8330 (pt) cc_final: 0.7900 (mp) REVERT: A 377 LEU cc_start: 0.7481 (mm) cc_final: 0.7203 (mt) REVERT: A 390 LEU cc_start: 0.8658 (tt) cc_final: 0.8455 (mt) REVERT: A 391 TYR cc_start: 0.7595 (m-10) cc_final: 0.7250 (m-10) REVERT: A 394 LYS cc_start: 0.7850 (tttm) cc_final: 0.7361 (tmmt) REVERT: A 395 TRP cc_start: 0.6544 (OUTLIER) cc_final: 0.5944 (m-90) REVERT: A 807 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6448 (tm-30) REVERT: A 838 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8727 (pp) REVERT: A 913 SER cc_start: 0.8478 (m) cc_final: 0.7874 (p) REVERT: A 1112 ARG cc_start: 0.7892 (ptp-110) cc_final: 0.7566 (ptp90) REVERT: A 1157 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8878 (ptm) REVERT: A 1189 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 1195 GLU cc_start: 0.7675 (pp20) cc_final: 0.7162 (pp20) REVERT: A 1335 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.7880 (p0) REVERT: A 1359 ARG cc_start: 0.5313 (mtt180) cc_final: 0.3851 (mtt180) REVERT: A 1411 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8332 (t0) REVERT: A 1810 TYR cc_start: 0.8973 (t80) cc_final: 0.8641 (t80) REVERT: A 1846 MET cc_start: 0.8628 (tpp) cc_final: 0.8376 (tpp) REVERT: A 2042 VAL cc_start: 0.7645 (OUTLIER) cc_final: 0.7338 (t) REVERT: A 2052 ASP cc_start: 0.8264 (t0) cc_final: 0.7881 (t0) REVERT: A 2202 GLU cc_start: 0.7128 (pm20) cc_final: 0.6873 (pp20) REVERT: A 2224 LYS cc_start: 0.8327 (ttpp) cc_final: 0.8081 (tmmt) REVERT: A 2225 PHE cc_start: 0.8135 (t80) cc_final: 0.7796 (t80) REVERT: A 2527 ASN cc_start: 0.8096 (t0) cc_final: 0.7825 (t0) REVERT: A 2542 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6864 (tm-30) REVERT: A 2546 CYS cc_start: 0.7091 (t) cc_final: 0.6815 (p) REVERT: A 2575 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6642 (mtp) REVERT: A 2598 MET cc_start: 0.5972 (mtt) cc_final: 0.5730 (mtt) REVERT: A 2609 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5275 (pp20) REVERT: A 2659 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 2726 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.7071 (mtt90) outliers start: 136 outliers final: 53 residues processed: 520 average time/residue: 1.3245 time to fit residues: 797.2384 Evaluate side-chains 474 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 401 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain B residue 1084 ASN Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1153 VAL Chi-restraints excluded: chain B residue 1161 SER Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1240 CYS Chi-restraints excluded: chain B residue 1316 ASP Chi-restraints excluded: chain B residue 1355 SER Chi-restraints excluded: chain B residue 1362 HIS Chi-restraints excluded: chain B residue 1382 CYS Chi-restraints excluded: chain B residue 1404 THR Chi-restraints excluded: chain B residue 1778 LEU Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1961 MET Chi-restraints excluded: chain B residue 2167 THR Chi-restraints excluded: chain B residue 2172 GLN Chi-restraints excluded: chain B residue 2198 ARG Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2256 MET Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2522 THR Chi-restraints excluded: chain B residue 2541 LEU Chi-restraints excluded: chain B residue 2546 CYS Chi-restraints excluded: chain B residue 2553 HIS Chi-restraints excluded: chain B residue 2600 LEU Chi-restraints excluded: chain B residue 2679 VAL Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2785 GLN Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 494 TRP Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 888 CYS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1411 ASN Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2252 ILE Chi-restraints excluded: chain A residue 2280 THR Chi-restraints excluded: chain A residue 2575 MET Chi-restraints excluded: chain A residue 2584 LEU Chi-restraints excluded: chain A residue 2609 GLU Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2725 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 241 optimal weight: 1.9990 chunk 197 optimal weight: 0.0870 chunk 79 optimal weight: 1.9990 chunk 290 optimal weight: 6.9990 chunk 313 optimal weight: 0.0870 chunk 258 optimal weight: 0.5980 chunk 287 optimal weight: 6.9990 chunk 98 optimal weight: 0.0980 chunk 232 optimal weight: 1.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2053 GLN B2055 HIS ** B2553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2652 HIS A 5 HIS A 909 GLN A1372 ASN A1385 HIS A2055 HIS ** A2253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2709 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25705 Z= 0.202 Angle : 0.698 12.210 34814 Z= 0.347 Chirality : 0.042 0.185 3956 Planarity : 0.005 0.058 4473 Dihedral : 5.983 110.479 3464 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.81 % Favored : 95.03 % Rotamer: Outliers : 4.64 % Allowed : 25.75 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.26 (0.15), residues: 3137 helix: 0.59 (0.15), residues: 1325 sheet: -0.14 (0.29), residues: 325 loop : -0.81 (0.17), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 765 HIS 0.011 0.001 HIS A 37 PHE 0.033 0.001 PHE B2568 TYR 0.017 0.001 TYR A 891 ARG 0.011 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 411 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 484 CYS cc_start: 0.8297 (t) cc_final: 0.8035 (t) REVERT: B 499 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.6038 (t80) REVERT: B 765 TRP cc_start: 0.7610 (t60) cc_final: 0.6787 (t60) REVERT: B 795 ASN cc_start: 0.7247 (t0) cc_final: 0.6878 (t0) REVERT: B 862 LYS cc_start: 0.7886 (mmmm) cc_final: 0.7608 (mmmt) REVERT: B 868 ILE cc_start: 0.8101 (mm) cc_final: 0.7830 (pp) REVERT: B 873 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7526 (tmmm) REVERT: B 890 GLN cc_start: 0.7381 (tp40) cc_final: 0.6833 (tp40) REVERT: B 914 HIS cc_start: 0.7755 (p90) cc_final: 0.7194 (p-80) REVERT: B 1124 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8296 (mtt90) REVERT: B 1152 ASP cc_start: 0.8047 (p0) cc_final: 0.7687 (p0) REVERT: B 1257 ARG cc_start: 0.8648 (mtt90) cc_final: 0.8432 (mtt90) REVERT: B 1316 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7401 (p0) REVERT: B 1362 HIS cc_start: 0.5665 (OUTLIER) cc_final: 0.5157 (t70) REVERT: B 1508 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7575 (tp-100) REVERT: B 1823 ASP cc_start: 0.7966 (t70) cc_final: 0.7644 (t0) REVERT: B 1833 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 1961 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7692 (tpp) REVERT: B 2172 GLN cc_start: 0.4801 (OUTLIER) cc_final: 0.4374 (tp-100) REVERT: B 2184 MET cc_start: 0.8423 (tpt) cc_final: 0.7983 (tmm) REVERT: B 2198 ARG cc_start: 0.7487 (ttt180) cc_final: 0.7221 (ttt180) REVERT: B 2256 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6090 (mmm) REVERT: B 2301 GLN cc_start: 0.7986 (tp40) cc_final: 0.7774 (tp-100) REVERT: B 2506 TYR cc_start: 0.7941 (p90) cc_final: 0.7695 (p90) REVERT: B 2522 THR cc_start: 0.7303 (OUTLIER) cc_final: 0.7048 (p) REVERT: B 2562 LYS cc_start: 0.7909 (tppt) cc_final: 0.7599 (tmmt) REVERT: B 2568 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7594 (t80) REVERT: B 2728 ASP cc_start: 0.7628 (t0) cc_final: 0.7259 (t0) REVERT: B 2736 SER cc_start: 0.7726 (t) cc_final: 0.6980 (p) REVERT: B 2749 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6896 (tpt) REVERT: A 11 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7029 (tp) REVERT: A 20 ASP cc_start: 0.7997 (m-30) cc_final: 0.7741 (m-30) REVERT: A 24 GLU cc_start: 0.7263 (mp0) cc_final: 0.7026 (mp0) REVERT: A 27 GLU cc_start: 0.7649 (pp20) cc_final: 0.7270 (pp20) REVERT: A 69 ARG cc_start: 0.6959 (tpt170) cc_final: 0.6664 (tpt-90) REVERT: A 372 ILE cc_start: 0.8335 (pt) cc_final: 0.7930 (mp) REVERT: A 395 TRP cc_start: 0.6509 (OUTLIER) cc_final: 0.5760 (m-90) REVERT: A 807 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6590 (tp30) REVERT: A 913 SER cc_start: 0.8522 (m) cc_final: 0.7827 (p) REVERT: A 1112 ARG cc_start: 0.7722 (ptp-110) cc_final: 0.7518 (ptp90) REVERT: A 1157 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8867 (ptm) REVERT: A 1195 GLU cc_start: 0.7749 (pp20) cc_final: 0.7137 (pp20) REVERT: A 1197 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.7971 (mtp85) REVERT: A 1335 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.7802 (p0) REVERT: A 1359 ARG cc_start: 0.5338 (mtt180) cc_final: 0.3985 (mtt180) REVERT: A 1799 MET cc_start: 0.8890 (mmt) cc_final: 0.8605 (mmp) REVERT: A 1810 TYR cc_start: 0.8960 (t80) cc_final: 0.8647 (t80) REVERT: A 1833 GLU cc_start: 0.7840 (pp20) cc_final: 0.7548 (OUTLIER) REVERT: A 2052 ASP cc_start: 0.8273 (t0) cc_final: 0.7900 (t0) REVERT: A 2224 LYS cc_start: 0.8284 (ttpp) cc_final: 0.8045 (tmmt) REVERT: A 2225 PHE cc_start: 0.8042 (t80) cc_final: 0.7722 (t80) REVERT: A 2546 CYS cc_start: 0.7093 (t) cc_final: 0.6857 (p) REVERT: A 2598 MET cc_start: 0.6042 (mtt) cc_final: 0.5803 (mtt) REVERT: A 2609 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5226 (pp20) REVERT: A 2626 VAL cc_start: 0.4513 (OUTLIER) cc_final: 0.4106 (m) REVERT: A 2633 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6695 (tm-30) REVERT: A 2676 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7870 (ttm-80) REVERT: A 2726 ARG cc_start: 0.7370 (mtt-85) cc_final: 0.7169 (mtt90) outliers start: 130 outliers final: 52 residues processed: 499 average time/residue: 1.3437 time to fit residues: 774.5623 Evaluate side-chains 464 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 395 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 499 PHE Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1155 MET Chi-restraints excluded: chain B residue 1240 CYS Chi-restraints excluded: chain B residue 1316 ASP Chi-restraints excluded: chain B residue 1355 SER Chi-restraints excluded: chain B residue 1362 HIS Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1961 MET Chi-restraints excluded: chain B residue 2172 GLN Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2256 MET Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2522 THR Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2541 LEU Chi-restraints excluded: chain B residue 2546 CYS Chi-restraints excluded: chain B residue 2553 HIS Chi-restraints excluded: chain B residue 2568 PHE Chi-restraints excluded: chain B residue 2679 VAL Chi-restraints excluded: chain B residue 2733 TRP Chi-restraints excluded: chain B residue 2749 MET Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2785 GLN Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 494 TRP Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 888 CYS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 2048 ILE Chi-restraints excluded: chain A residue 2055 HIS Chi-restraints excluded: chain A residue 2252 ILE Chi-restraints excluded: chain A residue 2280 THR Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2543 ASN Chi-restraints excluded: chain A residue 2584 LEU Chi-restraints excluded: chain A residue 2609 GLU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2689 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 150 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 308 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN B1326 GLN ** B2553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2697 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 ASN A1372 ASN A1385 HIS A2055 HIS ** A2253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2581 GLN A2652 HIS ** A2680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2709 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25705 Z= 0.393 Angle : 0.761 11.264 34814 Z= 0.381 Chirality : 0.046 0.204 3956 Planarity : 0.006 0.075 4473 Dihedral : 5.870 78.058 3452 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.96 % Favored : 93.88 % Rotamer: Outliers : 5.39 % Allowed : 25.46 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3137 helix: 0.43 (0.14), residues: 1331 sheet: -0.20 (0.28), residues: 334 loop : -0.97 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 765 HIS 0.015 0.002 HIS A2055 PHE 0.028 0.002 PHE A2571 TYR 0.024 0.002 TYR A 482 ARG 0.017 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 419 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 LEU cc_start: 0.7895 (mm) cc_final: 0.7695 (mp) REVERT: B 73 SER cc_start: 0.8274 (m) cc_final: 0.8043 (m) REVERT: B 484 CYS cc_start: 0.8448 (t) cc_final: 0.8245 (t) REVERT: B 780 GLN cc_start: 0.6769 (pm20) cc_final: 0.6503 (pm20) REVERT: B 795 ASN cc_start: 0.7364 (t0) cc_final: 0.7018 (t0) REVERT: B 838 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8719 (mp) REVERT: B 854 LEU cc_start: 0.3121 (OUTLIER) cc_final: 0.2673 (tm) REVERT: B 862 LYS cc_start: 0.7926 (mmmm) cc_final: 0.7689 (mmmt) REVERT: B 868 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7758 (pp) REVERT: B 873 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7569 (tmmm) REVERT: B 878 GLN cc_start: 0.7597 (tm-30) cc_final: 0.6517 (tm-30) REVERT: B 882 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6682 (ptt-90) REVERT: B 890 GLN cc_start: 0.7482 (tp40) cc_final: 0.7002 (tp40) REVERT: B 896 GLU cc_start: 0.6604 (tp30) cc_final: 0.6391 (tp30) REVERT: B 914 HIS cc_start: 0.7855 (p90) cc_final: 0.7266 (p-80) REVERT: B 1124 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8138 (mtm180) REVERT: B 1152 ASP cc_start: 0.7960 (p0) cc_final: 0.7634 (p0) REVERT: B 1248 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7957 (mmmt) REVERT: B 1508 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7682 (tp-100) REVERT: B 1833 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 1929 ASN cc_start: 0.8644 (t0) cc_final: 0.8296 (t0) REVERT: B 2044 LEU cc_start: 0.6876 (tm) cc_final: 0.6626 (tt) REVERT: B 2053 GLN cc_start: 0.7630 (pp30) cc_final: 0.7360 (pp30) REVERT: B 2058 GLN cc_start: 0.7671 (mm110) cc_final: 0.7429 (mp-120) REVERT: B 2062 ARG cc_start: 0.4562 (mmt180) cc_final: 0.3872 (mtm-85) REVERT: B 2064 GLU cc_start: 0.5365 (tp30) cc_final: 0.4965 (tp30) REVERT: B 2198 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6439 (ttp-170) REVERT: B 2256 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.6089 (mmm) REVERT: B 2301 GLN cc_start: 0.8171 (tp40) cc_final: 0.7831 (tp-100) REVERT: B 2506 TYR cc_start: 0.8009 (p90) cc_final: 0.7688 (p90) REVERT: B 2522 THR cc_start: 0.7344 (OUTLIER) cc_final: 0.7079 (p) REVERT: B 2562 LYS cc_start: 0.7929 (tppt) cc_final: 0.7606 (tmmt) REVERT: B 2568 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7546 (t80) REVERT: B 2643 MET cc_start: 0.7157 (mmt) cc_final: 0.6876 (mmp) REVERT: B 2686 ASN cc_start: 0.8192 (t0) cc_final: 0.7893 (t0) REVERT: B 2728 ASP cc_start: 0.7718 (t0) cc_final: 0.7250 (t0) REVERT: A 11 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7138 (tp) REVERT: A 24 GLU cc_start: 0.7174 (mp0) cc_final: 0.6907 (mp0) REVERT: A 69 ARG cc_start: 0.7244 (tpt170) cc_final: 0.6796 (tpt170) REVERT: A 359 ASP cc_start: 0.6461 (t0) cc_final: 0.6144 (t0) REVERT: A 372 ILE cc_start: 0.8665 (pt) cc_final: 0.8341 (mp) REVERT: A 377 LEU cc_start: 0.7447 (mm) cc_final: 0.7162 (mt) REVERT: A 394 LYS cc_start: 0.7868 (tttm) cc_final: 0.7485 (tmmt) REVERT: A 395 TRP cc_start: 0.6707 (OUTLIER) cc_final: 0.5924 (m-90) REVERT: A 494 TRP cc_start: 0.5613 (OUTLIER) cc_final: 0.3852 (t60) REVERT: A 733 ARG cc_start: 0.6398 (tpt170) cc_final: 0.5961 (tpm170) REVERT: A 807 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6479 (tp30) REVERT: A 873 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8134 (mppt) REVERT: A 913 SER cc_start: 0.8557 (m) cc_final: 0.7787 (p) REVERT: A 1195 GLU cc_start: 0.7909 (pp20) cc_final: 0.7341 (pp20) REVERT: A 1273 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: A 1359 ARG cc_start: 0.4988 (mtt180) cc_final: 0.4230 (mtt180) REVERT: A 1799 MET cc_start: 0.8865 (mmt) cc_final: 0.8613 (mmp) REVERT: A 1810 TYR cc_start: 0.9037 (t80) cc_final: 0.8722 (t80) REVERT: A 2052 ASP cc_start: 0.8364 (t0) cc_final: 0.7890 (t0) REVERT: A 2194 GLU cc_start: 0.7653 (pp20) cc_final: 0.7399 (pp20) REVERT: A 2221 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8443 (mtpt) REVERT: A 2225 PHE cc_start: 0.8106 (t80) cc_final: 0.7711 (t80) REVERT: A 2295 PHE cc_start: 0.8334 (t80) cc_final: 0.7997 (t80) REVERT: A 2598 MET cc_start: 0.6021 (mtt) cc_final: 0.5763 (mtt) REVERT: A 2609 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.5204 (pp20) REVERT: A 2633 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6841 (tm-30) REVERT: A 2726 ARG cc_start: 0.7464 (mtt-85) cc_final: 0.7257 (mtt90) outliers start: 151 outliers final: 77 residues processed: 527 average time/residue: 1.3457 time to fit residues: 821.2060 Evaluate side-chains 500 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 406 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1161 SER Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1240 CYS Chi-restraints excluded: chain B residue 1355 SER Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1404 THR Chi-restraints excluded: chain B residue 1801 LEU Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 2167 THR Chi-restraints excluded: chain B residue 2198 ARG Chi-restraints excluded: chain B residue 2256 MET Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2522 THR Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2541 LEU Chi-restraints excluded: chain B residue 2546 CYS Chi-restraints excluded: chain B residue 2553 HIS Chi-restraints excluded: chain B residue 2559 LEU Chi-restraints excluded: chain B residue 2568 PHE Chi-restraints excluded: chain B residue 2679 VAL Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2702 GLU Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2785 GLN Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 494 TRP Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 888 CYS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1273 GLU Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1411 ASN Chi-restraints excluded: chain A residue 1443 MET Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1911 MET Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 2252 ILE Chi-restraints excluded: chain A residue 2280 THR Chi-restraints excluded: chain A residue 2515 THR Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2584 LEU Chi-restraints excluded: chain A residue 2609 GLU Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2689 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 0.6980 chunk 175 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 263 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 157 optimal weight: 0.0670 chunk 276 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN B 890 GLN B1326 GLN ** B1362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2507 GLN ** B2553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2652 HIS ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 HIS ** A2253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2652 HIS ** A2680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2709 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25705 Z= 0.211 Angle : 0.714 11.446 34814 Z= 0.353 Chirality : 0.043 0.215 3956 Planarity : 0.005 0.070 4473 Dihedral : 5.326 57.477 3445 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.13 % Favored : 94.74 % Rotamer: Outliers : 4.39 % Allowed : 27.28 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.26 (0.15), residues: 3137 helix: 0.67 (0.15), residues: 1326 sheet: -0.12 (0.29), residues: 322 loop : -0.91 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 765 HIS 0.006 0.001 HIS B1362 PHE 0.024 0.001 PHE B2568 TYR 0.026 0.001 TYR B 378 ARG 0.009 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 414 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7696 (m-30) cc_final: 0.7495 (m-30) REVERT: B 73 SER cc_start: 0.8170 (m) cc_final: 0.7952 (m) REVERT: B 459 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: B 484 CYS cc_start: 0.8375 (t) cc_final: 0.8123 (t) REVERT: B 499 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.6164 (t80) REVERT: B 795 ASN cc_start: 0.7294 (t0) cc_final: 0.6924 (t0) REVERT: B 854 LEU cc_start: 0.1681 (OUTLIER) cc_final: 0.1214 (tm) REVERT: B 868 ILE cc_start: 0.7999 (mm) cc_final: 0.7764 (pp) REVERT: B 878 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6486 (tm-30) REVERT: B 882 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6742 (ptt-90) REVERT: B 890 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7051 (tp40) REVERT: B 914 HIS cc_start: 0.7739 (p90) cc_final: 0.7225 (p-80) REVERT: B 1091 LEU cc_start: 0.9198 (tp) cc_final: 0.8834 (pp) REVERT: B 1124 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8029 (mtm180) REVERT: B 1149 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7773 (ptpp) REVERT: B 1152 ASP cc_start: 0.7957 (p0) cc_final: 0.7422 (p0) REVERT: B 1248 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7835 (mmmt) REVERT: B 1508 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7639 (tp-100) REVERT: B 1833 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 2053 GLN cc_start: 0.7719 (pp30) cc_final: 0.7250 (pp30) REVERT: B 2058 GLN cc_start: 0.7592 (mm110) cc_final: 0.7385 (mp-120) REVERT: B 2064 GLU cc_start: 0.5216 (tp30) cc_final: 0.4817 (tp30) REVERT: B 2172 GLN cc_start: 0.4766 (OUTLIER) cc_final: 0.4265 (tp-100) REVERT: B 2184 MET cc_start: 0.8449 (tpt) cc_final: 0.8015 (tmm) REVERT: B 2198 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7147 (ttp-170) REVERT: B 2256 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.6059 (mmm) REVERT: B 2301 GLN cc_start: 0.8044 (tp40) cc_final: 0.7799 (tp-100) REVERT: B 2506 TYR cc_start: 0.7981 (p90) cc_final: 0.7600 (p90) REVERT: B 2522 THR cc_start: 0.7308 (OUTLIER) cc_final: 0.6758 (p) REVERT: B 2525 ARG cc_start: 0.6893 (tmm-80) cc_final: 0.6329 (ptt180) REVERT: B 2559 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7947 (tp) REVERT: B 2568 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7546 (t80) REVERT: B 2598 MET cc_start: 0.4717 (pmm) cc_final: 0.0488 (ppp) REVERT: B 2643 MET cc_start: 0.7111 (mmt) cc_final: 0.6812 (mmp) REVERT: B 2668 GLU cc_start: 0.5900 (pm20) cc_final: 0.5633 (pm20) REVERT: B 2676 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8043 (ttp-170) REVERT: B 2686 ASN cc_start: 0.8161 (t0) cc_final: 0.7859 (t0) REVERT: B 2736 SER cc_start: 0.7747 (t) cc_final: 0.7073 (p) REVERT: A 11 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7015 (tp) REVERT: A 16 ASP cc_start: 0.8104 (m-30) cc_final: 0.7904 (m-30) REVERT: A 20 ASP cc_start: 0.7910 (m-30) cc_final: 0.7514 (m-30) REVERT: A 24 GLU cc_start: 0.7072 (mp0) cc_final: 0.6797 (mp0) REVERT: A 28 LYS cc_start: 0.8149 (tmtt) cc_final: 0.7807 (tmtt) REVERT: A 29 LEU cc_start: 0.8754 (mt) cc_final: 0.8490 (tp) REVERT: A 69 ARG cc_start: 0.7069 (tpt170) cc_final: 0.6862 (tpt-90) REVERT: A 359 ASP cc_start: 0.6488 (t0) cc_final: 0.6165 (t0) REVERT: A 372 ILE cc_start: 0.8638 (pt) cc_final: 0.8372 (mp) REVERT: A 390 LEU cc_start: 0.8668 (tt) cc_final: 0.8408 (mt) REVERT: A 391 TYR cc_start: 0.7682 (m-10) cc_final: 0.7341 (m-10) REVERT: A 394 LYS cc_start: 0.7897 (tttm) cc_final: 0.7583 (tmmt) REVERT: A 395 TRP cc_start: 0.6521 (OUTLIER) cc_final: 0.5823 (m-90) REVERT: A 807 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6421 (tp30) REVERT: A 913 SER cc_start: 0.8625 (m) cc_final: 0.7948 (p) REVERT: A 915 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7713 (mmt180) REVERT: A 1157 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8763 (ptp) REVERT: A 1195 GLU cc_start: 0.7874 (pp20) cc_final: 0.7226 (pp20) REVERT: A 1197 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.7978 (mtp85) REVERT: A 1335 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.7799 (p0) REVERT: A 1359 ARG cc_start: 0.5637 (mtt180) cc_final: 0.4690 (mtt180) REVERT: A 1507 MET cc_start: 0.7933 (mmp) cc_final: 0.7724 (mmp) REVERT: A 1512 GLU cc_start: 0.7646 (mp0) cc_final: 0.7367 (mp0) REVERT: A 1799 MET cc_start: 0.8804 (mmt) cc_final: 0.8546 (mmp) REVERT: A 1810 TYR cc_start: 0.8976 (t80) cc_final: 0.8645 (t80) REVERT: A 1833 GLU cc_start: 0.7804 (pp20) cc_final: 0.7527 (pp20) REVERT: A 2052 ASP cc_start: 0.8283 (t0) cc_final: 0.7703 (t0) REVERT: A 2053 GLN cc_start: 0.7975 (mp10) cc_final: 0.7085 (mp10) REVERT: A 2194 GLU cc_start: 0.7624 (pp20) cc_final: 0.7329 (pp20) REVERT: A 2221 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8207 (mtpt) REVERT: A 2295 PHE cc_start: 0.8226 (t80) cc_final: 0.7899 (t80) REVERT: A 2609 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.5107 (pp20) REVERT: A 2626 VAL cc_start: 0.4462 (OUTLIER) cc_final: 0.4114 (m) REVERT: A 2633 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6831 (tm-30) REVERT: A 2726 ARG cc_start: 0.7405 (mtt-85) cc_final: 0.7122 (mtt90) outliers start: 123 outliers final: 63 residues processed: 495 average time/residue: 1.4836 time to fit residues: 853.0970 Evaluate side-chains 488 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 405 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 499 PHE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1240 CYS Chi-restraints excluded: chain B residue 1355 SER Chi-restraints excluded: chain B residue 1362 HIS Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 2172 GLN Chi-restraints excluded: chain B residue 2198 ARG Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2256 MET Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2522 THR Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2546 CYS Chi-restraints excluded: chain B residue 2553 HIS Chi-restraints excluded: chain B residue 2559 LEU Chi-restraints excluded: chain B residue 2568 PHE Chi-restraints excluded: chain B residue 2575 MET Chi-restraints excluded: chain B residue 2676 ARG Chi-restraints excluded: chain B residue 2679 VAL Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2702 GLU Chi-restraints excluded: chain B residue 2733 TRP Chi-restraints excluded: chain B residue 2785 GLN Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 888 CYS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1443 MET Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1911 MET Chi-restraints excluded: chain A residue 2056 LEU Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 2252 ILE Chi-restraints excluded: chain A residue 2280 THR Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2584 LEU Chi-restraints excluded: chain A residue 2609 GLU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2689 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 2.9990 chunk 277 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 0.0770 chunk 162 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN B1326 GLN ** B1362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2652 HIS ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 HIS A2055 HIS ** A2253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2652 HIS ** A2680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2709 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25705 Z= 0.250 Angle : 0.727 11.946 34814 Z= 0.359 Chirality : 0.043 0.213 3956 Planarity : 0.005 0.071 4473 Dihedral : 5.157 56.901 3439 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 4.35 % Allowed : 28.10 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.21 (0.15), residues: 3137 helix: 0.74 (0.15), residues: 1315 sheet: -0.15 (0.29), residues: 324 loop : -0.90 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 765 HIS 0.005 0.001 HIS A 37 PHE 0.031 0.002 PHE A2225 TYR 0.030 0.002 TYR A2296 ARG 0.010 0.001 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 412 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7773 (pmm) cc_final: 0.7560 (pmt) REVERT: B 73 SER cc_start: 0.8227 (m) cc_final: 0.8012 (m) REVERT: B 459 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7710 (pp20) REVERT: B 484 CYS cc_start: 0.8388 (t) cc_final: 0.8157 (t) REVERT: B 499 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.6208 (t80) REVERT: B 508 LYS cc_start: 0.2437 (OUTLIER) cc_final: 0.2039 (mppt) REVERT: B 555 ILE cc_start: -0.1558 (mt) cc_final: -0.1947 (mm) REVERT: B 795 ASN cc_start: 0.7249 (t0) cc_final: 0.6903 (t0) REVERT: B 838 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8689 (mp) REVERT: B 868 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7747 (pp) REVERT: B 878 GLN cc_start: 0.7560 (tm-30) cc_final: 0.6385 (tm-30) REVERT: B 882 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6782 (ptt-90) REVERT: B 890 GLN cc_start: 0.7489 (tp-100) cc_final: 0.7122 (tp40) REVERT: B 893 MET cc_start: 0.7729 (pmm) cc_final: 0.7182 (pmm) REVERT: B 914 HIS cc_start: 0.7746 (p90) cc_final: 0.7241 (p-80) REVERT: B 1091 LEU cc_start: 0.9205 (tp) cc_final: 0.8849 (pp) REVERT: B 1124 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8082 (mtm180) REVERT: B 1149 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7671 (ptpp) REVERT: B 1152 ASP cc_start: 0.7946 (p0) cc_final: 0.7382 (p0) REVERT: B 1248 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7817 (mmmt) REVERT: B 1508 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7712 (tp-100) REVERT: B 1833 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 2044 LEU cc_start: 0.6838 (tm) cc_final: 0.6594 (tt) REVERT: B 2053 GLN cc_start: 0.7766 (pp30) cc_final: 0.7224 (pp30) REVERT: B 2064 GLU cc_start: 0.5233 (tp30) cc_final: 0.4939 (tp30) REVERT: B 2184 MET cc_start: 0.8452 (tpt) cc_final: 0.8024 (tmm) REVERT: B 2198 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7108 (ttp-170) REVERT: B 2256 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.6150 (mmm) REVERT: B 2301 GLN cc_start: 0.8085 (tp40) cc_final: 0.7823 (tp-100) REVERT: B 2506 TYR cc_start: 0.8102 (p90) cc_final: 0.7828 (p90) REVERT: B 2522 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.6759 (p) REVERT: B 2525 ARG cc_start: 0.6898 (tmm-80) cc_final: 0.6335 (ptt180) REVERT: B 2542 GLN cc_start: 0.7672 (pm20) cc_final: 0.7386 (pm20) REVERT: B 2559 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7897 (tp) REVERT: B 2568 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7321 (t80) REVERT: B 2598 MET cc_start: 0.4728 (pmm) cc_final: 0.0522 (ppp) REVERT: B 2643 MET cc_start: 0.7109 (mmt) cc_final: 0.6805 (mmp) REVERT: B 2652 HIS cc_start: 0.7828 (t70) cc_final: 0.7613 (t-90) REVERT: B 2656 LYS cc_start: 0.7121 (mmtp) cc_final: 0.6861 (mmtm) REVERT: B 2676 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8043 (ttp-170) REVERT: B 2686 ASN cc_start: 0.8185 (t0) cc_final: 0.7804 (t0) REVERT: A 11 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7055 (tp) REVERT: A 16 ASP cc_start: 0.8136 (m-30) cc_final: 0.7888 (m-30) REVERT: A 20 ASP cc_start: 0.7962 (m-30) cc_final: 0.7462 (m-30) REVERT: A 24 GLU cc_start: 0.7089 (mp0) cc_final: 0.6756 (mp0) REVERT: A 69 ARG cc_start: 0.7076 (tpt170) cc_final: 0.6832 (tpt170) REVERT: A 359 ASP cc_start: 0.6615 (t0) cc_final: 0.6321 (t0) REVERT: A 372 ILE cc_start: 0.8682 (pt) cc_final: 0.8448 (mp) REVERT: A 395 TRP cc_start: 0.6585 (OUTLIER) cc_final: 0.5765 (m-90) REVERT: A 807 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6646 (tp30) REVERT: A 913 SER cc_start: 0.8624 (m) cc_final: 0.7951 (p) REVERT: A 915 ARG cc_start: 0.8101 (mmt-90) cc_final: 0.7730 (mmt180) REVERT: A 1195 GLU cc_start: 0.7926 (pp20) cc_final: 0.7282 (pp20) REVERT: A 1197 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7983 (mtp85) REVERT: A 1335 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.7854 (p0) REVERT: A 1359 ARG cc_start: 0.4898 (mtt180) cc_final: 0.3812 (mtt180) REVERT: A 1512 GLU cc_start: 0.7656 (mp0) cc_final: 0.7336 (mp0) REVERT: A 1799 MET cc_start: 0.8833 (mmt) cc_final: 0.8587 (mmp) REVERT: A 1810 TYR cc_start: 0.9013 (t80) cc_final: 0.8699 (t80) REVERT: A 1833 GLU cc_start: 0.7838 (pp20) cc_final: 0.7622 (pp20) REVERT: A 2052 ASP cc_start: 0.8285 (t0) cc_final: 0.7963 (t0) REVERT: A 2194 GLU cc_start: 0.7645 (pp20) cc_final: 0.7337 (pp20) REVERT: A 2202 GLU cc_start: 0.7211 (pm20) cc_final: 0.6995 (pp20) REVERT: A 2221 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8272 (mtpt) REVERT: A 2295 PHE cc_start: 0.8189 (t80) cc_final: 0.7953 (t80) REVERT: A 2609 GLU cc_start: 0.5326 (OUTLIER) cc_final: 0.5105 (pp20) REVERT: A 2626 VAL cc_start: 0.4808 (OUTLIER) cc_final: 0.4512 (m) REVERT: A 2675 PHE cc_start: 0.8165 (t80) cc_final: 0.7963 (t80) REVERT: A 2726 ARG cc_start: 0.7379 (mtt-85) cc_final: 0.7133 (mtp85) outliers start: 122 outliers final: 68 residues processed: 492 average time/residue: 1.4679 time to fit residues: 828.3330 Evaluate side-chains 487 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 399 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 499 PHE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 907 MET Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1240 CYS Chi-restraints excluded: chain B residue 1354 LEU Chi-restraints excluded: chain B residue 1362 HIS Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 2167 THR Chi-restraints excluded: chain B residue 2198 ARG Chi-restraints excluded: chain B residue 2222 GLU Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2256 MET Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2522 THR Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2546 CYS Chi-restraints excluded: chain B residue 2553 HIS Chi-restraints excluded: chain B residue 2559 LEU Chi-restraints excluded: chain B residue 2568 PHE Chi-restraints excluded: chain B residue 2575 MET Chi-restraints excluded: chain B residue 2676 ARG Chi-restraints excluded: chain B residue 2679 VAL Chi-restraints excluded: chain B residue 2685 VAL Chi-restraints excluded: chain B residue 2702 GLU Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2785 GLN Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 888 CYS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1443 MET Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1911 MET Chi-restraints excluded: chain A residue 2055 HIS Chi-restraints excluded: chain A residue 2056 LEU Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 2252 ILE Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2584 LEU Chi-restraints excluded: chain A residue 2609 GLU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2690 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 259 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS B1191 GLN B1326 GLN ** B1362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2652 HIS ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2055 HIS ** A2253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2652 HIS A2709 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25705 Z= 0.293 Angle : 0.750 13.654 34814 Z= 0.372 Chirality : 0.044 0.228 3956 Planarity : 0.005 0.072 4473 Dihedral : 5.186 54.749 3437 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.83 % Favored : 94.04 % Rotamer: Outliers : 4.71 % Allowed : 28.32 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.26 (0.15), residues: 3137 helix: 0.72 (0.15), residues: 1320 sheet: -0.25 (0.29), residues: 331 loop : -0.94 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 765 HIS 0.016 0.001 HIS A2055 PHE 0.031 0.002 PHE B2225 TYR 0.028 0.002 TYR B 378 ARG 0.010 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 410 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 SER cc_start: 0.8306 (m) cc_final: 0.8093 (m) REVERT: B 459 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7757 (pp20) REVERT: B 499 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6271 (t80) REVERT: B 795 ASN cc_start: 0.7249 (t0) cc_final: 0.6932 (t0) REVERT: B 838 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8702 (mp) REVERT: B 868 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7722 (pp) REVERT: B 878 GLN cc_start: 0.7556 (tm-30) cc_final: 0.6396 (tm-30) REVERT: B 882 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6838 (ptt-90) REVERT: B 890 GLN cc_start: 0.7532 (tp-100) cc_final: 0.7240 (tp40) REVERT: B 914 HIS cc_start: 0.7767 (p90) cc_final: 0.7229 (p-80) REVERT: B 1091 LEU cc_start: 0.9209 (tp) cc_final: 0.8862 (pp) REVERT: B 1124 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8092 (mtm180) REVERT: B 1149 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7630 (ptpp) REVERT: B 1152 ASP cc_start: 0.7967 (p0) cc_final: 0.7379 (p0) REVERT: B 1248 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7768 (mmmt) REVERT: B 1508 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7690 (tp-100) REVERT: B 1833 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 1961 MET cc_start: 0.7797 (tpp) cc_final: 0.7466 (tpp) REVERT: B 2044 LEU cc_start: 0.6931 (tm) cc_final: 0.6710 (tt) REVERT: B 2053 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.6990 (pp30) REVERT: B 2064 GLU cc_start: 0.5256 (tp30) cc_final: 0.4950 (tp30) REVERT: B 2184 MET cc_start: 0.8460 (tpt) cc_final: 0.8025 (tmm) REVERT: B 2256 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6376 (mmm) REVERT: B 2301 GLN cc_start: 0.8096 (tp40) cc_final: 0.7876 (tp-100) REVERT: B 2506 TYR cc_start: 0.8128 (p90) cc_final: 0.7837 (p90) REVERT: B 2522 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6551 (p) REVERT: B 2523 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6755 (tm-30) REVERT: B 2525 ARG cc_start: 0.6875 (tmm-80) cc_final: 0.6350 (ptt180) REVERT: B 2559 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7944 (tp) REVERT: B 2562 LYS cc_start: 0.7447 (tmmt) cc_final: 0.7180 (tmmt) REVERT: B 2568 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7325 (t80) REVERT: B 2598 MET cc_start: 0.4778 (pmm) cc_final: 0.0937 (ppp) REVERT: B 2643 MET cc_start: 0.7114 (mmt) cc_final: 0.6812 (mmp) REVERT: B 2686 ASN cc_start: 0.8173 (t0) cc_final: 0.7848 (t0) REVERT: A 11 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7132 (tp) REVERT: A 20 ASP cc_start: 0.7968 (m-30) cc_final: 0.7599 (m-30) REVERT: A 24 GLU cc_start: 0.7113 (mp0) cc_final: 0.6771 (mp0) REVERT: A 359 ASP cc_start: 0.6736 (t0) cc_final: 0.6454 (t0) REVERT: A 372 ILE cc_start: 0.8741 (pt) cc_final: 0.8519 (mp) REVERT: A 390 LEU cc_start: 0.8580 (tt) cc_final: 0.8363 (mt) REVERT: A 391 TYR cc_start: 0.7506 (m-10) cc_final: 0.7108 (m-10) REVERT: A 494 TRP cc_start: 0.5455 (OUTLIER) cc_final: 0.4281 (t60) REVERT: A 733 ARG cc_start: 0.6373 (tpt170) cc_final: 0.5626 (tpm170) REVERT: A 807 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6488 (tp30) REVERT: A 913 SER cc_start: 0.8642 (m) cc_final: 0.7971 (p) REVERT: A 915 ARG cc_start: 0.8092 (mmt-90) cc_final: 0.7734 (mmt180) REVERT: A 1086 HIS cc_start: 0.5797 (OUTLIER) cc_final: 0.5526 (p-80) REVERT: A 1187 GLU cc_start: 0.7394 (pm20) cc_final: 0.7015 (pm20) REVERT: A 1195 GLU cc_start: 0.7981 (pp20) cc_final: 0.7343 (pp20) REVERT: A 1197 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.8000 (mtp85) REVERT: A 1335 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.7870 (p0) REVERT: A 1359 ARG cc_start: 0.5004 (mtt180) cc_final: 0.3905 (mtt180) REVERT: A 1512 GLU cc_start: 0.7676 (mp0) cc_final: 0.7318 (mp0) REVERT: A 1799 MET cc_start: 0.8840 (mmt) cc_final: 0.8609 (mmp) REVERT: A 1810 TYR cc_start: 0.9020 (t80) cc_final: 0.8696 (t80) REVERT: A 1833 GLU cc_start: 0.7864 (pp20) cc_final: 0.7624 (pp20) REVERT: A 2052 ASP cc_start: 0.8301 (t0) cc_final: 0.7941 (t0) REVERT: A 2194 GLU cc_start: 0.7642 (pp20) cc_final: 0.7310 (pp20) REVERT: A 2202 GLU cc_start: 0.7289 (pm20) cc_final: 0.7038 (pp20) REVERT: A 2221 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8289 (mtpt) REVERT: A 2295 PHE cc_start: 0.8185 (t80) cc_final: 0.7953 (t80) REVERT: A 2609 GLU cc_start: 0.5324 (OUTLIER) cc_final: 0.5108 (pp20) REVERT: A 2626 VAL cc_start: 0.4809 (OUTLIER) cc_final: 0.4516 (m) REVERT: A 2633 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6607 (pp20) outliers start: 132 outliers final: 73 residues processed: 496 average time/residue: 1.4018 time to fit residues: 799.1990 Evaluate side-chains 497 residues out of total 2808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 405 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 499 PHE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 841 ILE Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 907 MET Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 938 THR Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1161 SER Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1240 CYS Chi-restraints excluded: chain B residue 1354 LEU Chi-restraints excluded: chain B residue 1362 HIS Chi-restraints excluded: chain B residue 1377 THR Chi-restraints excluded: chain B residue 1838 THR Chi-restraints excluded: chain B residue 1939 LEU Chi-restraints excluded: chain B residue 2053 GLN Chi-restraints excluded: chain B residue 2167 THR Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2256 MET Chi-restraints excluded: chain B residue 2272 MET Chi-restraints excluded: chain B residue 2522 THR Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2546 CYS Chi-restraints excluded: chain B residue 2553 HIS Chi-restraints excluded: chain B residue 2559 LEU Chi-restraints excluded: chain B residue 2568 PHE Chi-restraints excluded: chain B residue 2575 MET Chi-restraints excluded: chain B residue 2679 VAL Chi-restraints excluded: chain B residue 2702 GLU Chi-restraints excluded: chain B residue 2762 LEU Chi-restraints excluded: chain B residue 2774 VAL Chi-restraints excluded: chain B residue 2785 GLN Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 494 TRP Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 888 CYS Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1086 HIS Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1335 ASP Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1443 MET Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1488 MET Chi-restraints excluded: chain A residue 1911 MET Chi-restraints excluded: chain A residue 2056 LEU Chi-restraints excluded: chain A residue 2221 LYS Chi-restraints excluded: chain A residue 2252 ILE Chi-restraints excluded: chain A residue 2280 THR Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2584 LEU Chi-restraints excluded: chain A residue 2609 GLU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2689 MET Chi-restraints excluded: chain A residue 2690 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 209 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: