Starting phenix.real_space_refine on Thu Mar 14 18:27:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/03_2024/8ubr_42101_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/03_2024/8ubr_42101.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/03_2024/8ubr_42101_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/03_2024/8ubr_42101_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/03_2024/8ubr_42101_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/03_2024/8ubr_42101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/03_2024/8ubr_42101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/03_2024/8ubr_42101_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubr_42101/03_2024/8ubr_42101_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 6180 2.51 5 N 1547 2.21 5 O 1653 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 873": "OE1" <-> "OE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1152": "OD1" <-> "OD2" Residue "A ASP 1154": "OD1" <-> "OD2" Residue "A GLU 1228": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A ASP 1275": "OD1" <-> "OD2" Residue "A GLU 1308": "OE1" <-> "OE2" Residue "A GLU 1314": "OE1" <-> "OE2" Residue "A ASP 1341": "OD1" <-> "OD2" Residue "A ASP 1394": "OD1" <-> "OD2" Residue "A GLU 1401": "OE1" <-> "OE2" Residue "A GLU 1405": "OE1" <-> "OE2" Residue "A ASP 1425": "OD1" <-> "OD2" Residue "A PHE 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9440 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9265 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 30, 'TRANS': 1125} Chain breaks: 6 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 175 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 2, 'LBN': 2, 'WG5': 1} Classifications: {'undetermined': 9, 'water': 4} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'LBN:plan-2': 2, 'LBN:plan-3': 2, 'LBN:plan-1': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 5.46, per 1000 atoms: 0.58 Number of scatterers: 9440 At special positions: 0 Unit cell: (75.712, 87.204, 142.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1653 8.00 N 1547 7.00 C 6180 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: 3.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 5 sheets defined 64.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.583A pdb=" N ARG A 21 " --> pdb=" O SER A 18 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.638A pdb=" N LYS A 26 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 69 through 108 removed outlier: 6.848A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 119 through 166 removed outlier: 3.737A pdb=" N PHE A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.539A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.602A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 267 removed outlier: 4.029A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TRP A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 4.032A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ALA A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N CYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 278 through 312 removed outlier: 3.736A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 removed outlier: 3.612A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.783A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.950A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 538 No H-bonds generated for 'chain 'A' and resid 536 through 538' Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 857 through 885 Processing helix chain 'A' and resid 913 through 926 removed outlier: 4.764A pdb=" N ASP A 924 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 958 Processing helix chain 'A' and resid 961 through 966 removed outlier: 4.639A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 984 removed outlier: 3.723A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1011 removed outlier: 3.915A pdb=" N VAL A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1060 Proline residue: A1021 - end of helix removed outlier: 3.877A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix Processing helix chain 'A' and resid 1062 through 1068 Processing helix chain 'A' and resid 1071 through 1120 removed outlier: 4.018A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1167 removed outlier: 3.962A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.608A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1285 removed outlier: 3.889A pdb=" N ALA A1285 " --> pdb=" O GLN A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1321 Processing helix chain 'A' and resid 1325 through 1330 removed outlier: 3.550A pdb=" N GLN A1330 " --> pdb=" O SER A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1361 Processing helix chain 'A' and resid 1378 through 1390 removed outlier: 4.535A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1409 Processing helix chain 'A' and resid 1427 through 1432 Processing helix chain 'A' and resid 1435 through 1440 Processing helix chain 'A' and resid 1443 through 1449 Processing sheet with id= A, first strand: chain 'A' and resid 446 through 448 removed outlier: 3.511A pdb=" N PHE A 446 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 624 through 628 removed outlier: 6.538A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG A 600 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL A 456 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 602 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1266 through 1269 removed outlier: 5.368A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1216 through 1218 Processing sheet with id= E, first strand: chain 'A' and resid 1420 through 1424 removed outlier: 6.630A pdb=" N VAL A1397 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU A1242 " --> pdb=" O VAL A1397 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A1399 " --> pdb=" O LEU A1242 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1521 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: 3.02 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1592 1.32 - 1.45: 2466 1.45 - 1.57: 5490 1.57 - 1.69: 11 1.69 - 1.81: 81 Bond restraints: 9640 Sorted by residual: bond pdb=" C10 WG5 A1508 " pdb=" C8 WG5 A1508 " ideal model delta sigma weight residual 1.791 1.477 0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C10 WG5 A1508 " pdb=" S21 WG5 A1508 " ideal model delta sigma weight residual 1.447 1.732 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C22 WG5 A1508 " pdb=" N7 WG5 A1508 " ideal model delta sigma weight residual 1.604 1.374 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C11 WG5 A1508 " pdb=" C12 WG5 A1508 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 ... (remaining 9635 not shown) Histogram of bond angle deviations from ideal: 92.94 - 101.37: 35 101.37 - 109.80: 1090 109.80 - 118.23: 6527 118.23 - 126.66: 5257 126.66 - 135.09: 143 Bond angle restraints: 13052 Sorted by residual: angle pdb=" C10 WG5 A1508 " pdb=" C11 WG5 A1508 " pdb=" C12 WG5 A1508 " ideal model delta sigma weight residual 152.65 131.64 21.01 3.00e+00 1.11e-01 4.90e+01 angle pdb=" C11 WG5 A1508 " pdb=" C10 WG5 A1508 " pdb=" C8 WG5 A1508 " ideal model delta sigma weight residual 101.66 120.28 -18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 133.72 6.15 1.00e+00 1.00e+00 3.79e+01 angle pdb=" PB ATP A1502 " pdb=" O3B ATP A1502 " pdb=" PG ATP A1502 " ideal model delta sigma weight residual 139.87 135.09 4.78 1.00e+00 1.00e+00 2.29e+01 angle pdb=" C10 WG5 A1508 " pdb=" S21 WG5 A1508 " pdb=" C22 WG5 A1508 " ideal model delta sigma weight residual 105.84 92.94 12.90 3.00e+00 1.11e-01 1.85e+01 ... (remaining 13047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.47: 5095 19.47 - 38.93: 555 38.93 - 58.40: 152 58.40 - 77.86: 28 77.86 - 97.33: 11 Dihedral angle restraints: 5841 sinusoidal: 2482 harmonic: 3359 Sorted by residual: dihedral pdb=" C32 LBN A1505 " pdb=" C33 LBN A1505 " pdb=" C4 LBN A1505 " pdb=" C7 LBN A1505 " ideal model delta sinusoidal sigma weight residual 179.89 -82.78 -97.33 1 3.00e+01 1.11e-03 1.20e+01 dihedral pdb=" CB GLU A1228 " pdb=" CG GLU A1228 " pdb=" CD GLU A1228 " pdb=" OE1 GLU A1228 " ideal model delta sinusoidal sigma weight residual 0.00 89.01 -89.01 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASP A 579 " pdb=" CB ASP A 579 " pdb=" CG ASP A 579 " pdb=" OD1 ASP A 579 " ideal model delta sinusoidal sigma weight residual -30.00 -85.48 55.48 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 5838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1206 0.062 - 0.123: 227 0.123 - 0.185: 59 0.185 - 0.246: 14 0.246 - 0.308: 1 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA ILE A 906 " pdb=" N ILE A 906 " pdb=" C ILE A 906 " pdb=" CB ILE A 906 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LYS A 329 " pdb=" N LYS A 329 " pdb=" C LYS A 329 " pdb=" CB LYS A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA CYS A1344 " pdb=" N CYS A1344 " pdb=" C CYS A1344 " pdb=" CB CYS A1344 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1504 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1009 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" C ALA A1009 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA A1009 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL A1010 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 WG5 A1508 " -0.013 2.00e-02 2.50e+03 1.65e-02 6.84e+00 pdb=" C11 WG5 A1508 " 0.020 2.00e-02 2.50e+03 pdb=" C12 WG5 A1508 " -0.003 2.00e-02 2.50e+03 pdb=" C22 WG5 A1508 " -0.003 2.00e-02 2.50e+03 pdb=" C5 WG5 A1508 " -0.024 2.00e-02 2.50e+03 pdb=" C8 WG5 A1508 " 0.003 2.00e-02 2.50e+03 pdb=" N7 WG5 A1508 " 0.003 2.00e-02 2.50e+03 pdb=" O9 WG5 A1508 " 0.013 2.00e-02 2.50e+03 pdb=" S21 WG5 A1508 " -0.024 2.00e-02 2.50e+03 pdb=" S23 WG5 A1508 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 WG5 A1508 " -0.029 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" C12 WG5 A1508 " 0.014 2.00e-02 2.50e+03 pdb=" C13 WG5 A1508 " 0.012 2.00e-02 2.50e+03 pdb=" C14 WG5 A1508 " 0.005 2.00e-02 2.50e+03 pdb=" C15 WG5 A1508 " 0.001 2.00e-02 2.50e+03 pdb=" C16 WG5 A1508 " 0.005 2.00e-02 2.50e+03 pdb=" C17 WG5 A1508 " 0.011 2.00e-02 2.50e+03 pdb=" C18 WG5 A1508 " -0.019 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 13 2.49 - 3.09: 6380 3.09 - 3.69: 13756 3.69 - 4.30: 20848 4.30 - 4.90: 34106 Nonbonded interactions: 75103 Sorted by model distance: nonbonded pdb=" O3G ATP A1503 " pdb="MG MG A1509 " model vdw 1.887 2.170 nonbonded pdb="MG MG A1509 " pdb=" O HOH A1602 " model vdw 1.904 2.170 nonbonded pdb="MG MG A1509 " pdb=" O HOH A1601 " model vdw 1.926 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1509 " model vdw 2.009 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.045 2.170 ... (remaining 75098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.010 Extract box with map and model: 18.180 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.670 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:14.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.008 0.314 9640 Z= 0.528 Angle : 0.893 21.010 13052 Z= 0.577 Chirality : 0.056 0.308 1507 Planarity : 0.004 0.031 1573 Dihedral : 17.655 97.329 3669 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.10 % Allowed : 19.82 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1142 helix: 1.32 (0.19), residues: 757 sheet: -1.22 (0.44), residues: 88 loop : -0.95 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1063 HIS 0.005 0.001 HIS A 939 PHE 0.019 0.002 PHE A 446 TYR 0.024 0.002 TYR A 38 ARG 0.007 0.001 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.044 Fit side-chains REVERT: A 536 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7329 (mppt) REVERT: A 1010 VAL cc_start: 0.6843 (t) cc_final: 0.6636 (t) REVERT: A 1109 ILE cc_start: 0.7663 (mt) cc_final: 0.7325 (tt) REVERT: A 1341 ASP cc_start: 0.7051 (t0) cc_final: 0.6699 (t70) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 1.3147 time to fit residues: 193.6487 Evaluate side-chains 108 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1166 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.0060 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN A1224 ASN A1423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9640 Z= 0.154 Angle : 0.515 15.698 13052 Z= 0.266 Chirality : 0.038 0.126 1507 Planarity : 0.003 0.032 1573 Dihedral : 8.650 62.769 1467 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.25 % Allowed : 19.92 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1142 helix: 2.14 (0.19), residues: 761 sheet: -0.31 (0.49), residues: 92 loop : -0.78 (0.31), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 865 HIS 0.003 0.001 HIS A 949 PHE 0.011 0.001 PHE A1257 TYR 0.013 0.001 TYR A1073 ARG 0.005 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.070 Fit side-chains REVERT: A 36 ASP cc_start: 0.7888 (m-30) cc_final: 0.7459 (m-30) REVERT: A 47 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6541 (p0) REVERT: A 373 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6725 (t0) REVERT: A 476 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: A 479 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: A 536 LYS cc_start: 0.7616 (mmtt) cc_final: 0.7412 (mppt) REVERT: A 1010 VAL cc_start: 0.6781 (t) cc_final: 0.6502 (t) REVERT: A 1091 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8405 (tt) REVERT: A 1109 ILE cc_start: 0.7608 (mt) cc_final: 0.7246 (tt) REVERT: A 1137 MET cc_start: 0.6999 (tpp) cc_final: 0.6759 (tpt) REVERT: A 1317 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7131 (tttp) REVERT: A 1341 ASP cc_start: 0.7100 (t0) cc_final: 0.6724 (t70) REVERT: A 1405 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6559 (mp0) outliers start: 33 outliers final: 10 residues processed: 136 average time/residue: 1.2497 time to fit residues: 182.2600 Evaluate side-chains 120 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1390 GLN Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 HIS A1224 ASN A1375 HIS A1402 HIS A1428 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9640 Z= 0.295 Angle : 0.660 13.580 13052 Z= 0.341 Chirality : 0.044 0.143 1507 Planarity : 0.005 0.042 1573 Dihedral : 8.709 71.568 1467 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.64 % Allowed : 18.54 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1142 helix: 1.74 (0.18), residues: 759 sheet: 0.10 (0.51), residues: 90 loop : -0.96 (0.30), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1063 HIS 0.006 0.002 HIS A 856 PHE 0.017 0.002 PHE A 976 TYR 0.018 0.002 TYR A1073 ARG 0.005 0.001 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 109 time to evaluate : 0.932 Fit side-chains REVERT: A 47 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6654 (p0) REVERT: A 279 GLU cc_start: 0.7037 (mp0) cc_final: 0.6720 (mp0) REVERT: A 286 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7431 (mm-30) REVERT: A 476 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 483 LYS cc_start: 0.7769 (mtmp) cc_final: 0.7534 (mtmm) REVERT: A 536 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7509 (mmmm) REVERT: A 1091 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 1109 ILE cc_start: 0.7756 (mt) cc_final: 0.7428 (tt) REVERT: A 1165 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7768 (mmtm) REVERT: A 1309 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: A 1341 ASP cc_start: 0.7319 (t0) cc_final: 0.6931 (t70) outliers start: 47 outliers final: 14 residues processed: 144 average time/residue: 1.3321 time to fit residues: 204.6208 Evaluate side-chains 120 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9640 Z= 0.180 Angle : 0.537 14.077 13052 Z= 0.277 Chirality : 0.039 0.126 1507 Planarity : 0.004 0.030 1573 Dihedral : 8.338 69.453 1467 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.73 % Allowed : 19.63 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1142 helix: 2.02 (0.19), residues: 759 sheet: 0.28 (0.52), residues: 92 loop : -0.84 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 865 HIS 0.003 0.001 HIS A 939 PHE 0.012 0.001 PHE A 446 TYR 0.016 0.001 TYR A 917 ARG 0.004 0.000 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 107 time to evaluate : 1.056 Fit side-chains REVERT: A 47 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6743 (p0) REVERT: A 373 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6722 (t0) REVERT: A 384 GLU cc_start: 0.3582 (OUTLIER) cc_final: 0.2881 (pm20) REVERT: A 476 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 483 LYS cc_start: 0.7737 (mtmp) cc_final: 0.7508 (mtmm) REVERT: A 1091 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 1109 ILE cc_start: 0.7751 (mt) cc_final: 0.7396 (tt) REVERT: A 1120 LEU cc_start: 0.7023 (mm) cc_final: 0.6822 (mm) REVERT: A 1165 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7671 (mmtm) REVERT: A 1309 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: A 1317 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7208 (tttp) REVERT: A 1341 ASP cc_start: 0.7206 (t0) cc_final: 0.6820 (t70) REVERT: A 1405 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6674 (mp0) outliers start: 48 outliers final: 20 residues processed: 141 average time/residue: 1.2586 time to fit residues: 189.6974 Evaluate side-chains 128 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1317 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 0.1980 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A1224 ASN A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9640 Z= 0.249 Angle : 0.602 13.731 13052 Z= 0.309 Chirality : 0.041 0.131 1507 Planarity : 0.004 0.034 1573 Dihedral : 8.381 71.450 1467 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.44 % Allowed : 20.41 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1142 helix: 1.83 (0.19), residues: 754 sheet: 0.18 (0.50), residues: 92 loop : -0.87 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1063 HIS 0.004 0.001 HIS A 949 PHE 0.014 0.002 PHE A 446 TYR 0.018 0.002 TYR A 917 ARG 0.004 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 100 time to evaluate : 1.144 Fit side-chains REVERT: A 47 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6672 (p0) REVERT: A 279 GLU cc_start: 0.6991 (mp0) cc_final: 0.6639 (mp0) REVERT: A 286 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7267 (mm-30) REVERT: A 373 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6724 (t0) REVERT: A 384 GLU cc_start: 0.3611 (OUTLIER) cc_final: 0.2388 (pm20) REVERT: A 476 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: A 483 LYS cc_start: 0.7789 (mtmp) cc_final: 0.7546 (mtmm) REVERT: A 536 LYS cc_start: 0.7669 (mmmm) cc_final: 0.7316 (mmtp) REVERT: A 1091 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 1109 ILE cc_start: 0.7735 (mt) cc_final: 0.7414 (tt) REVERT: A 1120 LEU cc_start: 0.7149 (mm) cc_final: 0.6938 (mm) REVERT: A 1165 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7744 (mmtm) REVERT: A 1341 ASP cc_start: 0.7319 (t0) cc_final: 0.6919 (t70) REVERT: A 1351 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8137 (mttm) outliers start: 45 outliers final: 24 residues processed: 132 average time/residue: 1.2445 time to fit residues: 175.9608 Evaluate side-chains 128 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1351 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 92 optimal weight: 0.0030 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9640 Z= 0.156 Angle : 0.508 13.781 13052 Z= 0.261 Chirality : 0.038 0.127 1507 Planarity : 0.003 0.030 1573 Dihedral : 7.989 68.298 1467 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.75 % Allowed : 21.30 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1142 helix: 2.13 (0.19), residues: 760 sheet: 0.37 (0.51), residues: 92 loop : -0.82 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1063 HIS 0.003 0.001 HIS A 939 PHE 0.010 0.001 PHE A 446 TYR 0.014 0.001 TYR A1073 ARG 0.004 0.000 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 1.093 Fit side-chains REVERT: A 47 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6690 (p0) REVERT: A 286 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 373 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6750 (t0) REVERT: A 384 GLU cc_start: 0.3640 (OUTLIER) cc_final: 0.2876 (pm20) REVERT: A 476 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 483 LYS cc_start: 0.7782 (mtmp) cc_final: 0.7552 (mtmm) REVERT: A 536 LYS cc_start: 0.7661 (mmmm) cc_final: 0.7402 (mmtp) REVERT: A 1091 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8279 (tt) REVERT: A 1109 ILE cc_start: 0.7647 (mt) cc_final: 0.7313 (tt) REVERT: A 1120 LEU cc_start: 0.7125 (mm) cc_final: 0.6913 (mm) REVERT: A 1165 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7657 (mmtm) REVERT: A 1317 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7122 (tttp) REVERT: A 1341 ASP cc_start: 0.7214 (t0) cc_final: 0.6832 (t70) outliers start: 38 outliers final: 20 residues processed: 128 average time/residue: 1.2847 time to fit residues: 176.6036 Evaluate side-chains 126 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1317 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS A1224 ASN A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9640 Z= 0.330 Angle : 0.671 13.558 13052 Z= 0.345 Chirality : 0.044 0.179 1507 Planarity : 0.005 0.041 1573 Dihedral : 8.496 72.845 1467 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.73 % Allowed : 21.10 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.24), residues: 1142 helix: 1.62 (0.19), residues: 755 sheet: 0.19 (0.50), residues: 92 loop : -0.92 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1063 HIS 0.005 0.002 HIS A 949 PHE 0.017 0.002 PHE A1296 TYR 0.019 0.002 TYR A 917 ARG 0.005 0.001 ARG A 975 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 98 time to evaluate : 1.134 Fit side-chains REVERT: A 47 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6696 (p0) REVERT: A 279 GLU cc_start: 0.7054 (mp0) cc_final: 0.6751 (mp0) REVERT: A 286 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 384 GLU cc_start: 0.3639 (OUTLIER) cc_final: 0.2831 (pm20) REVERT: A 476 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: A 483 LYS cc_start: 0.7829 (mtmp) cc_final: 0.7580 (mtmm) REVERT: A 536 LYS cc_start: 0.7645 (mmmm) cc_final: 0.7400 (mmtm) REVERT: A 1091 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8278 (tt) REVERT: A 1109 ILE cc_start: 0.7754 (mt) cc_final: 0.7431 (tt) REVERT: A 1165 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7807 (mmtm) REVERT: A 1341 ASP cc_start: 0.7331 (t0) cc_final: 0.6921 (t70) REVERT: A 1351 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8127 (mttm) outliers start: 48 outliers final: 31 residues processed: 135 average time/residue: 1.2016 time to fit residues: 173.9848 Evaluate side-chains 130 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 93 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1351 LYS Chi-restraints excluded: chain A residue 1415 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 75 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9640 Z= 0.169 Angle : 0.538 13.839 13052 Z= 0.278 Chirality : 0.039 0.145 1507 Planarity : 0.003 0.031 1573 Dihedral : 8.170 68.969 1467 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.85 % Allowed : 22.19 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.25), residues: 1142 helix: 2.01 (0.19), residues: 754 sheet: 0.38 (0.51), residues: 92 loop : -0.79 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1063 HIS 0.003 0.001 HIS A 939 PHE 0.010 0.001 PHE A 446 TYR 0.016 0.001 TYR A 917 ARG 0.003 0.000 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 97 time to evaluate : 0.890 Fit side-chains REVERT: A 47 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6691 (p0) REVERT: A 188 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7356 (tp) REVERT: A 279 GLU cc_start: 0.6933 (mp0) cc_final: 0.6583 (mp0) REVERT: A 384 GLU cc_start: 0.3623 (OUTLIER) cc_final: 0.2847 (pm20) REVERT: A 476 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 483 LYS cc_start: 0.7776 (mtmp) cc_final: 0.7535 (mtmm) REVERT: A 536 LYS cc_start: 0.7626 (mmmm) cc_final: 0.7356 (mmtp) REVERT: A 1091 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8278 (tt) REVERT: A 1109 ILE cc_start: 0.7672 (mt) cc_final: 0.7351 (tt) REVERT: A 1165 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7708 (mmtm) REVERT: A 1317 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7141 (tttp) REVERT: A 1341 ASP cc_start: 0.7282 (t0) cc_final: 0.6886 (t70) REVERT: A 1405 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6667 (mp0) outliers start: 39 outliers final: 21 residues processed: 127 average time/residue: 1.3067 time to fit residues: 177.1176 Evaluate side-chains 125 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 81 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9640 Z= 0.157 Angle : 0.521 13.613 13052 Z= 0.267 Chirality : 0.038 0.147 1507 Planarity : 0.003 0.030 1573 Dihedral : 7.864 67.207 1467 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.55 % Allowed : 22.09 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.25), residues: 1142 helix: 2.15 (0.19), residues: 760 sheet: 0.45 (0.52), residues: 92 loop : -0.74 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1063 HIS 0.003 0.001 HIS A 939 PHE 0.011 0.001 PHE A 81 TYR 0.016 0.001 TYR A 917 ARG 0.005 0.000 ARG A1422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 1.170 Fit side-chains REVERT: A 47 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6689 (p0) REVERT: A 384 GLU cc_start: 0.3616 (OUTLIER) cc_final: 0.2810 (pm20) REVERT: A 476 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: A 536 LYS cc_start: 0.7638 (mmmm) cc_final: 0.7376 (mmtp) REVERT: A 1091 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8256 (tt) REVERT: A 1109 ILE cc_start: 0.7631 (mt) cc_final: 0.7277 (tt) REVERT: A 1317 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7099 (tttp) REVERT: A 1341 ASP cc_start: 0.7249 (t0) cc_final: 0.6871 (t70) REVERT: A 1405 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6647 (mp0) outliers start: 36 outliers final: 19 residues processed: 125 average time/residue: 1.2503 time to fit residues: 167.2984 Evaluate side-chains 119 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1224 ASN A1428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9640 Z= 0.318 Angle : 0.667 13.525 13052 Z= 0.340 Chirality : 0.044 0.185 1507 Planarity : 0.005 0.040 1573 Dihedral : 8.402 72.269 1467 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.25 % Allowed : 22.88 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1142 helix: 1.65 (0.19), residues: 754 sheet: 0.32 (0.51), residues: 92 loop : -0.91 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1063 HIS 0.005 0.002 HIS A 949 PHE 0.016 0.002 PHE A1296 TYR 0.018 0.002 TYR A 917 ARG 0.007 0.001 ARG A1422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 1.089 Fit side-chains REVERT: A 47 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6676 (p0) REVERT: A 279 GLU cc_start: 0.7045 (mp0) cc_final: 0.6715 (mp0) REVERT: A 286 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 384 GLU cc_start: 0.3710 (OUTLIER) cc_final: 0.2866 (pm20) REVERT: A 476 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: A 483 LYS cc_start: 0.7848 (mtmp) cc_final: 0.7601 (mtmm) REVERT: A 598 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7721 (mmtt) REVERT: A 1091 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8269 (tt) REVERT: A 1109 ILE cc_start: 0.7730 (mt) cc_final: 0.7413 (tt) REVERT: A 1341 ASP cc_start: 0.7328 (t0) cc_final: 0.6928 (t70) REVERT: A 1405 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6780 (mp0) outliers start: 33 outliers final: 21 residues processed: 120 average time/residue: 1.2860 time to fit residues: 165.1906 Evaluate side-chains 120 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1317 LYS Chi-restraints excluded: chain A residue 1405 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1038 GLN A1224 ASN A1428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109144 restraints weight = 11780.135| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.33 r_work: 0.3139 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9640 Z= 0.153 Angle : 0.518 13.791 13052 Z= 0.265 Chirality : 0.038 0.137 1507 Planarity : 0.003 0.030 1573 Dihedral : 7.911 66.969 1467 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 23.18 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.25), residues: 1142 helix: 2.06 (0.19), residues: 761 sheet: 0.51 (0.52), residues: 92 loop : -0.79 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A1063 HIS 0.003 0.001 HIS A 939 PHE 0.010 0.001 PHE A 446 TYR 0.014 0.001 TYR A1073 ARG 0.005 0.000 ARG A1422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3693.06 seconds wall clock time: 65 minutes 54.24 seconds (3954.24 seconds total)