Starting phenix.real_space_refine on Tue Mar 3 18:54:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pz9_20528/03_2026/6pz9_20528_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pz9_20528/03_2026/6pz9_20528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pz9_20528/03_2026/6pz9_20528_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pz9_20528/03_2026/6pz9_20528_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pz9_20528/03_2026/6pz9_20528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pz9_20528/03_2026/6pz9_20528.map" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.009 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 P 3 5.49 5 S 26 5.16 5 C 4940 2.51 5 N 1411 2.21 5 O 1393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7773 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 7612 Classifications: {'peptide': 1177} Incomplete info: {'truncation_to_alanine': 512} Link IDs: {'PTRANS': 37, 'TRANS': 1139} Chain breaks: 6 Unresolved non-hydrogen bonds: 1666 Unresolved non-hydrogen angles: 2111 Unresolved non-hydrogen dihedrals: 1298 Unresolved non-hydrogen chiralities: 217 Planarities with less than four sites: {'ASP:plan': 39, 'ARG:plan': 29, 'GLN:plan1': 30, 'GLU:plan': 37, 'ASN:plan1': 22, 'TYR:plan': 4, 'PHE:plan': 17, 'HIS:plan': 5, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 778 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 97 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ATP': 1, 'BJX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BJX C1601 " occ=0.00 ... (31 atoms not shown) pdb=" O3 BJX C1601 " occ=0.00 Time building chain proxies: 2.28, per 1000 atoms: 0.29 Number of scatterers: 7773 At special positions: 0 Unit cell: (97.185, 85.69, 131.67, 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) S 26 16.00 P 3 15.00 O 1393 8.00 N 1411 7.00 C 4940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 340.5 milliseconds 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 68.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.956A pdb=" N GLY C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.947A pdb=" N LYS C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 277 Processing helix chain 'C' and resid 283 through 326 removed outlier: 5.870A pdb=" N ARG C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Proline residue: C 317 - end of helix Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 355 through 400 removed outlier: 3.506A pdb=" N ALA C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 413 through 422 removed outlier: 3.571A pdb=" N ILE C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 434 removed outlier: 3.704A pdb=" N ASN C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 431 " --> pdb=" O GLN C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 456 removed outlier: 3.717A pdb=" N LEU C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 457 through 469 removed outlier: 3.759A pdb=" N LEU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 505 removed outlier: 3.644A pdb=" N VAL C 477 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 512 Processing helix chain 'C' and resid 514 through 539 removed outlier: 4.322A pdb=" N PHE C 518 " --> pdb=" O TRP C 514 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 524 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 525 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 535 " --> pdb=" O THR C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 565 Proline residue: C 551 - end of helix Processing helix chain 'C' and resid 572 through 614 removed outlier: 3.988A pdb=" N ALA C 578 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 581 " --> pdb=" O PHE C 577 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C 588 " --> pdb=" O HIS C 584 " (cutoff:3.500A) Proline residue: C 589 - end of helix removed outlier: 3.896A pdb=" N SER C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 599 " --> pdb=" O SER C 595 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 603 " --> pdb=" O SER C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 728 removed outlier: 3.562A pdb=" N LEU C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 790 Processing helix chain 'C' and resid 795 through 806 Processing helix chain 'C' and resid 807 through 815 removed outlier: 4.308A pdb=" N ASP C 811 " --> pdb=" O SER C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 821 removed outlier: 3.823A pdb=" N GLN C 820 " --> pdb=" O HIS C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 846 removed outlier: 3.722A pdb=" N ALA C 843 " --> pdb=" O SER C 839 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 844 " --> pdb=" O VAL C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 881 removed outlier: 3.605A pdb=" N GLU C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.523A pdb=" N PHE C 917 " --> pdb=" O THR C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 928 Processing helix chain 'C' and resid 996 through 1008 removed outlier: 4.086A pdb=" N SER C1006 " --> pdb=" O THR C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1039 removed outlier: 4.704A pdb=" N LEU C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C1021 " --> pdb=" O VAL C1017 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL C1028 " --> pdb=" O HIS C1024 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP C1031 " --> pdb=" O LEU C1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C1038 " --> pdb=" O LEU C1034 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C1039 " --> pdb=" O ALA C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1103 removed outlier: 3.516A pdb=" N LEU C1070 " --> pdb=" O MET C1066 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU C1074 " --> pdb=" O LEU C1070 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C1087 " --> pdb=" O SER C1083 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG C1096 " --> pdb=" O LYS C1092 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER C1100 " --> pdb=" O ARG C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1116 removed outlier: 3.605A pdb=" N PHE C1113 " --> pdb=" O PRO C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1117 through 1135 removed outlier: 3.765A pdb=" N ASP C1128 " --> pdb=" O ARG C1124 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1161 removed outlier: 3.625A pdb=" N THR C1139 " --> pdb=" O HIS C1135 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU C1148 " --> pdb=" O SER C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1210 removed outlier: 3.952A pdb=" N ALA C1167 " --> pdb=" O VAL C1163 " (cutoff:3.500A) Proline residue: C1170 - end of helix removed outlier: 3.650A pdb=" N VAL C1173 " --> pdb=" O LEU C1169 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C1184 " --> pdb=" O LYS C1180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C1185 " --> pdb=" O TYR C1181 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP C1188 " --> pdb=" O VAL C1184 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C1198 " --> pdb=" O ASP C1194 " (cutoff:3.500A) Proline residue: C1199 - end of helix removed outlier: 4.117A pdb=" N VAL C1208 " --> pdb=" O PHE C1204 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C1210 " --> pdb=" O GLU C1206 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1217 removed outlier: 3.865A pdb=" N ILE C1214 " --> pdb=" O GLY C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1219 through 1272 removed outlier: 3.737A pdb=" N PHE C1223 " --> pdb=" O TYR C1219 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C1225 " --> pdb=" O ALA C1221 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C1226 " --> pdb=" O ARG C1222 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C1227 " --> pdb=" O PHE C1223 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C1232 " --> pdb=" O LEU C1228 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C1236 " --> pdb=" O ASP C1232 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C1237 " --> pdb=" O SER C1233 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C1240 " --> pdb=" O ILE C1236 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C1241 " --> pdb=" O ALA C1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 1281 through 1292 removed outlier: 3.945A pdb=" N LEU C1289 " --> pdb=" O LEU C1285 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C1292 " --> pdb=" O ALA C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1294 through 1319 removed outlier: 3.948A pdb=" N ALA C1311 " --> pdb=" O ILE C1307 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL C1312 " --> pdb=" O GLN C1308 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C1313 " --> pdb=" O LEU C1309 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C1314 " --> pdb=" O GLY C1310 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C1315 " --> pdb=" O ALA C1311 " (cutoff:3.500A) Processing helix chain 'C' and resid 1384 through 1392 removed outlier: 3.583A pdb=" N PHE C1392 " --> pdb=" O PHE C1388 " (cutoff:3.500A) Processing helix chain 'C' and resid 1411 through 1413 No H-bonds generated for 'chain 'C' and resid 1411 through 1413' Processing helix chain 'C' and resid 1414 through 1421 Processing helix chain 'C' and resid 1435 through 1441 Processing helix chain 'C' and resid 1448 through 1459 removed outlier: 3.748A pdb=" N ALA C1458 " --> pdb=" O ALA C1454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C1459 " --> pdb=" O LEU C1455 " (cutoff:3.500A) Processing helix chain 'C' and resid 1460 through 1466 Processing helix chain 'C' and resid 1484 through 1499 removed outlier: 3.991A pdb=" N GLN C1488 " --> pdb=" O GLN C1484 " (cutoff:3.500A) Processing helix chain 'C' and resid 1512 through 1531 Processing helix chain 'C' and resid 1565 through 1570 removed outlier: 3.725A pdb=" N GLN C1569 " --> pdb=" O THR C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1570 through 1578 Processing sheet with id=AA1, first strand: chain 'C' and resid 680 through 681 Processing sheet with id=AA2, first strand: chain 'C' and resid 685 through 687 removed outlier: 7.148A pdb=" N THR C 687 " --> pdb=" O LYS C 732 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS C 732 " --> pdb=" O THR C 687 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AA4, first strand: chain 'C' and resid 901 through 904 removed outlier: 7.233A pdb=" N ALA C 902 " --> pdb=" O GLN C 909 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1360 through 1368 removed outlier: 6.856A pdb=" N VAL C1352 " --> pdb=" O VAL C1361 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS C1363 " --> pdb=" O LEU C1350 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C1350 " --> pdb=" O LYS C1363 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C1365 " --> pdb=" O GLN C1348 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN C1348 " --> pdb=" O VAL C1365 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR C1367 " --> pdb=" O GLN C1346 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN C1346 " --> pdb=" O THR C1367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 1423 through 1425 removed outlier: 6.136A pdb=" N SER C1423 " --> pdb=" O ILE C1504 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 1549 through 1552 545 hydrogen bonds defined for protein. 1605 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: 1.35 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1273 1.31 - 1.43: 2104 1.43 - 1.56: 4499 1.56 - 1.69: 5 1.69 - 1.81: 40 Bond restraints: 7921 Sorted by residual: bond pdb=" C4 ATP C1602 " pdb=" C5 ATP C1602 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.63e+01 bond pdb=" C5 ATP C1602 " pdb=" C6 ATP C1602 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.50e+01 bond pdb=" C4 ATP C1602 " pdb=" N9 ATP C1602 " ideal model delta sigma weight residual 1.374 1.316 0.058 1.00e-02 1.00e+04 3.42e+01 bond pdb=" C16 BJX C1601 " pdb=" N1 BJX C1601 " ideal model delta sigma weight residual 1.344 1.448 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C5 ATP C1602 " pdb=" N7 ATP C1602 " ideal model delta sigma weight residual 1.387 1.336 0.051 1.00e-02 1.00e+04 2.56e+01 ... (remaining 7916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 10729 4.02 - 8.04: 150 8.04 - 12.06: 13 12.06 - 16.09: 3 16.09 - 20.11: 2 Bond angle restraints: 10897 Sorted by residual: angle pdb=" PA ATP C1602 " pdb=" O3A ATP C1602 " pdb=" PB ATP C1602 " ideal model delta sigma weight residual 136.83 116.72 20.11 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP C1602 " pdb=" O3B ATP C1602 " pdb=" PG ATP C1602 " ideal model delta sigma weight residual 139.87 120.87 19.00 1.00e+00 1.00e+00 3.61e+02 angle pdb=" N LYS D 5 " pdb=" CA LYS D 5 " pdb=" C LYS D 5 " ideal model delta sigma weight residual 110.88 101.94 8.94 1.28e+00 6.10e-01 4.88e+01 angle pdb=" C5 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N3 ATP C1602 " ideal model delta sigma weight residual 126.80 120.16 6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" N3 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N9 ATP C1602 " ideal model delta sigma weight residual 127.04 133.58 -6.54 1.15e+00 7.59e-01 3.25e+01 ... (remaining 10892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 4555 30.81 - 61.63: 59 61.63 - 92.44: 11 92.44 - 123.25: 3 123.25 - 154.06: 1 Dihedral angle restraints: 4629 sinusoidal: 1147 harmonic: 3482 Sorted by residual: dihedral pdb=" CA SER C 280 " pdb=" C SER C 280 " pdb=" N PRO C 281 " pdb=" CA PRO C 281 " ideal model delta harmonic sigma weight residual -180.00 -146.85 -33.15 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA ALA C1331 " pdb=" C ALA C1331 " pdb=" N PRO C1332 " pdb=" CA PRO C1332 " ideal model delta harmonic sigma weight residual 180.00 -148.46 -31.54 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA PHE C1528 " pdb=" C PHE C1528 " pdb=" N ALA C1529 " pdb=" CA ALA C1529 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 4626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 969 0.065 - 0.130: 311 0.130 - 0.195: 47 0.195 - 0.260: 4 0.260 - 0.325: 5 Chirality restraints: 1336 Sorted by residual: chirality pdb=" CG LEU C1248 " pdb=" CB LEU C1248 " pdb=" CD1 LEU C1248 " pdb=" CD2 LEU C1248 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C5 BJX C1601 " pdb=" C7 BJX C1601 " pdb=" C8 BJX C1601 " pdb=" N1 BJX C1601 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE C1255 " pdb=" CA ILE C1255 " pdb=" CG1 ILE C1255 " pdb=" CG2 ILE C1255 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1333 not shown) Planarity restraints: 1419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1037 " -0.028 2.00e-02 2.50e+03 2.90e-02 2.10e+01 pdb=" CG TRP C1037 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP C1037 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C1037 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1037 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C1037 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1037 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1037 " -0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP C1037 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 243 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO C 244 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 244 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 244 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 316 " -0.055 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO C 317 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 317 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 317 " -0.045 5.00e-02 4.00e+02 ... (remaining 1416 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 877 2.74 - 3.28: 7920 3.28 - 3.82: 12439 3.82 - 4.36: 13674 4.36 - 4.90: 23327 Nonbonded interactions: 58237 Sorted by model distance: nonbonded pdb=" OG1 THR C 371 " pdb=" OH TYR C1254 " model vdw 2.205 3.040 nonbonded pdb=" N ASN C 781 " pdb=" OE2 GLU C1206 " model vdw 2.227 3.120 nonbonded pdb=" O SER C 302 " pdb=" OG SER C 376 " model vdw 2.249 3.040 nonbonded pdb=" O LEU C1192 " pdb=" OG1 THR C1196 " model vdw 2.256 3.040 nonbonded pdb=" O THR C1161 " pdb=" OG1 THR C1161 " model vdw 2.262 3.040 ... (remaining 58232 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.170 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 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 : 0.009 0.104 7921 Z= 0.429 Angle : 1.214 20.108 10897 Z= 0.709 Chirality : 0.064 0.325 1336 Planarity : 0.009 0.084 1419 Dihedral : 12.970 154.064 2359 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.20), residues: 1180 helix: -2.02 (0.15), residues: 763 sheet: -2.96 (0.59), residues: 67 loop : -3.38 (0.27), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 388 TYR 0.040 0.004 TYR C1219 PHE 0.050 0.005 PHE C 432 TRP 0.069 0.006 TRP C1037 HIS 0.011 0.002 HIS C1098 Details of bonding type rmsd covalent geometry : bond 0.00903 ( 7921) covalent geometry : angle 1.21367 (10897) hydrogen bonds : bond 0.25553 ( 545) hydrogen bonds : angle 9.01541 ( 1605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.283 Fit side-chains REVERT: C 300 ILE cc_start: 0.8328 (mm) cc_final: 0.8003 (mt) REVERT: C 302 SER cc_start: 0.8600 (p) cc_final: 0.8315 (t) REVERT: C 368 LEU cc_start: 0.9183 (mm) cc_final: 0.8953 (mp) REVERT: C 424 ASP cc_start: 0.8160 (t70) cc_final: 0.7854 (t70) REVERT: C 1154 LEU cc_start: 0.8115 (mm) cc_final: 0.7885 (mt) REVERT: C 1268 ILE cc_start: 0.5943 (mt) cc_final: 0.5676 (mm) REVERT: C 1306 GLU cc_start: 0.7648 (tp30) cc_final: 0.7290 (tp30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0831 time to fit residues: 21.1667 Evaluate side-chains 127 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 50.0000 chunk 117 optimal weight: 8.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN C 374 GLN C 562 HIS C 896 HIS C1098 HIS C1273 HIS C1316 HIS C1364 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.157694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.139148 restraints weight = 14824.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.142343 restraints weight = 6776.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.144365 restraints weight = 3867.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.145644 restraints weight = 2605.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.146446 restraints weight = 1977.596| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7921 Z= 0.220 Angle : 0.717 10.129 10897 Z= 0.376 Chirality : 0.047 0.352 1336 Planarity : 0.006 0.062 1419 Dihedral : 10.642 153.972 1301 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.72 % Allowed : 11.59 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.23), residues: 1180 helix: -0.66 (0.18), residues: 786 sheet: -2.66 (0.60), residues: 69 loop : -3.05 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 486 TYR 0.019 0.002 TYR C1032 PHE 0.032 0.002 PHE C 432 TRP 0.024 0.003 TRP C1037 HIS 0.008 0.002 HIS C1098 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 7921) covalent geometry : angle 0.71696 (10897) hydrogen bonds : bond 0.04384 ( 545) hydrogen bonds : angle 5.10689 ( 1605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.271 Fit side-chains REVERT: C 412 MET cc_start: 0.7022 (ptp) cc_final: 0.6699 (ptp) REVERT: C 429 MET cc_start: 0.8626 (ttm) cc_final: 0.8391 (ttm) REVERT: C 451 LEU cc_start: 0.5429 (pp) cc_final: 0.4901 (mp) REVERT: C 770 VAL cc_start: 0.9273 (t) cc_final: 0.8871 (p) REVERT: C 1168 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.6806 (tp) outliers start: 24 outliers final: 18 residues processed: 159 average time/residue: 0.0643 time to fit residues: 15.2599 Evaluate side-chains 136 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 1027 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.157647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.138917 restraints weight = 14490.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.142040 restraints weight = 6645.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.143999 restraints weight = 3798.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.145219 restraints weight = 2567.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146014 restraints weight = 1966.644| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7921 Z= 0.203 Angle : 0.670 10.024 10897 Z= 0.344 Chirality : 0.046 0.296 1336 Planarity : 0.005 0.057 1419 Dihedral : 10.144 156.845 1301 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 6.48 % Allowed : 14.34 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.24), residues: 1180 helix: -0.13 (0.18), residues: 788 sheet: -2.55 (0.62), residues: 69 loop : -2.98 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 598 TYR 0.017 0.002 TYR C 378 PHE 0.025 0.002 PHE C 321 TRP 0.033 0.002 TRP C1037 HIS 0.004 0.001 HIS C1098 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 7921) covalent geometry : angle 0.66958 (10897) hydrogen bonds : bond 0.04198 ( 545) hydrogen bonds : angle 4.79475 ( 1605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: C 253 LEU cc_start: 0.8171 (tm) cc_final: 0.7928 (tp) REVERT: C 412 MET cc_start: 0.6922 (ptp) cc_final: 0.6567 (ptp) REVERT: C 424 ASP cc_start: 0.8126 (t70) cc_final: 0.7915 (t70) REVERT: C 451 LEU cc_start: 0.5653 (pp) cc_final: 0.5016 (mp) REVERT: C 598 ARG cc_start: 0.8026 (ttm110) cc_final: 0.7694 (mtp85) REVERT: C 896 HIS cc_start: 0.3576 (m90) cc_final: 0.3156 (t-90) REVERT: C 1168 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7027 (tp) REVERT: C 1190 GLN cc_start: 0.8703 (tp40) cc_final: 0.8290 (mt0) outliers start: 33 outliers final: 22 residues processed: 151 average time/residue: 0.0555 time to fit residues: 12.8103 Evaluate side-chains 144 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1302 LEU Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 114 optimal weight: 40.0000 chunk 91 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.150943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132133 restraints weight = 15246.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135123 restraints weight = 7099.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137030 restraints weight = 4110.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.138233 restraints weight = 2819.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.138961 restraints weight = 2190.342| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 7921 Z= 0.343 Angle : 0.816 11.085 10897 Z= 0.428 Chirality : 0.051 0.304 1336 Planarity : 0.006 0.061 1419 Dihedral : 10.402 156.905 1301 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 8.06 % Allowed : 17.29 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.24), residues: 1180 helix: -0.51 (0.18), residues: 777 sheet: -2.93 (0.62), residues: 67 loop : -2.94 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 486 TYR 0.023 0.003 TYR C1219 PHE 0.041 0.003 PHE C 321 TRP 0.032 0.003 TRP C1037 HIS 0.010 0.002 HIS C 867 Details of bonding type rmsd covalent geometry : bond 0.00730 ( 7921) covalent geometry : angle 0.81585 (10897) hydrogen bonds : bond 0.04957 ( 545) hydrogen bonds : angle 5.39285 ( 1605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: C 412 MET cc_start: 0.6966 (ptp) cc_final: 0.6579 (ptp) REVERT: C 424 ASP cc_start: 0.8293 (t70) cc_final: 0.8048 (t70) REVERT: C 1191 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: C 1206 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7650 (mt-10) outliers start: 41 outliers final: 36 residues processed: 159 average time/residue: 0.0539 time to fit residues: 13.0207 Evaluate side-chains 161 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1151 VAL Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1289 LEU Chi-restraints excluded: chain C residue 1294 TYR Chi-restraints excluded: chain C residue 1302 LEU Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 2 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 100 optimal weight: 50.0000 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 113 optimal weight: 50.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.153699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.135125 restraints weight = 15068.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.138148 restraints weight = 6972.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140077 restraints weight = 4029.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.141248 restraints weight = 2740.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.142024 restraints weight = 2128.820| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 7921 Z= 0.240 Angle : 0.701 11.326 10897 Z= 0.361 Chirality : 0.047 0.288 1336 Planarity : 0.005 0.054 1419 Dihedral : 10.185 158.214 1301 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 8.45 % Allowed : 17.88 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.24), residues: 1180 helix: -0.21 (0.19), residues: 778 sheet: -2.59 (0.63), residues: 69 loop : -2.82 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 598 TYR 0.020 0.002 TYR C1219 PHE 0.032 0.002 PHE C 351 TRP 0.021 0.002 TRP C1037 HIS 0.004 0.001 HIS C1364 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 7921) covalent geometry : angle 0.70128 (10897) hydrogen bonds : bond 0.04191 ( 545) hydrogen bonds : angle 4.96385 ( 1605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: C 253 LEU cc_start: 0.8262 (tp) cc_final: 0.7769 (tp) REVERT: C 412 MET cc_start: 0.6937 (ptp) cc_final: 0.6545 (ptp) REVERT: C 475 TYR cc_start: 0.8644 (t80) cc_final: 0.8056 (t80) REVERT: C 598 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7682 (mtp85) REVERT: C 1068 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7147 (t80) REVERT: C 1125 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7415 (t80) REVERT: C 1168 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7201 (tp) REVERT: C 1191 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: C 1206 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 1213 THR cc_start: 0.9139 (m) cc_final: 0.8867 (p) REVERT: C 1261 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8650 (tt) outliers start: 43 outliers final: 32 residues processed: 159 average time/residue: 0.0473 time to fit residues: 11.8005 Evaluate side-chains 162 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1125 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1151 VAL Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1261 LEU Chi-restraints excluded: chain C residue 1291 VAL Chi-restraints excluded: chain C residue 1294 TYR Chi-restraints excluded: chain C residue 1302 LEU Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 61 optimal weight: 50.0000 chunk 70 optimal weight: 7.9990 chunk 58 optimal weight: 40.0000 chunk 50 optimal weight: 40.0000 chunk 105 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 397 ASN C1197 GLN C1234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.154783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.135782 restraints weight = 15068.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.138912 restraints weight = 7045.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.140901 restraints weight = 4098.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.142162 restraints weight = 2805.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.142833 restraints weight = 2175.245| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7921 Z= 0.164 Angle : 0.624 10.190 10897 Z= 0.318 Chirality : 0.044 0.289 1336 Planarity : 0.004 0.050 1419 Dihedral : 9.885 159.268 1301 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 8.25 % Allowed : 21.02 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.25), residues: 1180 helix: 0.15 (0.19), residues: 790 sheet: -2.35 (0.65), residues: 69 loop : -2.92 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 598 TYR 0.015 0.002 TYR C 378 PHE 0.027 0.001 PHE C 351 TRP 0.016 0.002 TRP C1037 HIS 0.005 0.001 HIS C 863 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7921) covalent geometry : angle 0.62443 (10897) hydrogen bonds : bond 0.03718 ( 545) hydrogen bonds : angle 4.55229 ( 1605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: C 253 LEU cc_start: 0.8126 (tp) cc_final: 0.7672 (tp) REVERT: C 263 TYR cc_start: 0.8642 (t80) cc_final: 0.8440 (t80) REVERT: C 367 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8752 (mp) REVERT: C 392 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: C 412 MET cc_start: 0.6856 (ptp) cc_final: 0.6477 (ptp) REVERT: C 475 TYR cc_start: 0.8558 (t80) cc_final: 0.7968 (t80) REVERT: C 598 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7697 (mtp85) REVERT: C 1068 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7063 (t80) REVERT: C 1125 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7468 (t80) REVERT: C 1168 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7137 (tp) REVERT: C 1190 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: C 1191 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: C 1206 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7536 (mt-10) REVERT: C 1261 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8603 (tt) outliers start: 42 outliers final: 33 residues processed: 154 average time/residue: 0.0648 time to fit residues: 14.9999 Evaluate side-chains 165 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 889 HIS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1125 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1190 GLN Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1250 VAL Chi-restraints excluded: chain C residue 1261 LEU Chi-restraints excluded: chain C residue 1291 VAL Chi-restraints excluded: chain C residue 1294 TYR Chi-restraints excluded: chain C residue 1302 LEU Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 7.9990 chunk 114 optimal weight: 40.0000 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.158718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.140116 restraints weight = 14455.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143297 restraints weight = 6760.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.145329 restraints weight = 3877.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.146560 restraints weight = 2611.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.147317 restraints weight = 2002.379| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7921 Z= 0.131 Angle : 0.584 9.984 10897 Z= 0.294 Chirality : 0.043 0.258 1336 Planarity : 0.004 0.054 1419 Dihedral : 9.712 161.353 1301 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.88 % Allowed : 22.99 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.25), residues: 1180 helix: 0.58 (0.19), residues: 791 sheet: -2.09 (0.67), residues: 69 loop : -2.86 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 598 TYR 0.018 0.001 TYR C 377 PHE 0.023 0.001 PHE C 351 TRP 0.015 0.001 TRP C1037 HIS 0.002 0.001 HIS C1024 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7921) covalent geometry : angle 0.58424 (10897) hydrogen bonds : bond 0.03398 ( 545) hydrogen bonds : angle 4.21049 ( 1605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.243 Fit side-chains REVERT: C 233 MET cc_start: 0.7619 (tpp) cc_final: 0.6839 (tpp) REVERT: C 392 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: C 412 MET cc_start: 0.6857 (ptp) cc_final: 0.6537 (ptp) REVERT: C 475 TYR cc_start: 0.8580 (t80) cc_final: 0.7947 (t80) REVERT: C 598 ARG cc_start: 0.8066 (ttm110) cc_final: 0.7648 (mtp85) REVERT: C 1068 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7235 (t80) REVERT: C 1190 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: C 1191 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: C 1206 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7529 (mt-10) REVERT: C 1261 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8550 (tt) outliers start: 35 outliers final: 26 residues processed: 149 average time/residue: 0.0604 time to fit residues: 13.7794 Evaluate side-chains 153 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 889 HIS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1190 GLN Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1261 LEU Chi-restraints excluded: chain C residue 1291 VAL Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 0.0570 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 97 optimal weight: 0.0050 chunk 12 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 114 optimal weight: 40.0000 overall best weight: 1.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.161759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.143187 restraints weight = 14432.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.146371 restraints weight = 6818.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.148420 restraints weight = 3954.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.149678 restraints weight = 2680.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.150335 restraints weight = 2043.381| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 7921 Z= 0.111 Angle : 0.576 9.911 10897 Z= 0.287 Chirality : 0.042 0.260 1336 Planarity : 0.004 0.055 1419 Dihedral : 9.494 161.162 1301 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.30 % Allowed : 25.15 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1180 helix: 0.92 (0.19), residues: 792 sheet: -1.85 (0.71), residues: 68 loop : -2.73 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 598 TYR 0.017 0.001 TYR C 377 PHE 0.021 0.001 PHE C 351 TRP 0.014 0.001 TRP C1037 HIS 0.003 0.001 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7921) covalent geometry : angle 0.57562 (10897) hydrogen bonds : bond 0.03246 ( 545) hydrogen bonds : angle 4.03012 ( 1605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 233 MET cc_start: 0.7546 (tpp) cc_final: 0.6768 (tpp) REVERT: C 367 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8703 (mp) REVERT: C 475 TYR cc_start: 0.8445 (t80) cc_final: 0.7828 (t80) REVERT: C 598 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7465 (mtp85) REVERT: C 1068 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.7216 (t80) REVERT: C 1190 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: C 1191 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: C 1206 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7521 (mt-10) REVERT: C 1261 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8538 (tt) REVERT: C 1272 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5440 (mp) REVERT: C 1290 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6206 (mpp) REVERT: C 1305 MET cc_start: 0.8222 (tpp) cc_final: 0.7989 (tpp) outliers start: 27 outliers final: 17 residues processed: 148 average time/residue: 0.0679 time to fit residues: 15.0320 Evaluate side-chains 141 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 889 HIS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1190 GLN Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1253 GLU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1261 LEU Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1291 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.0570 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.164273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.145647 restraints weight = 14170.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.148873 restraints weight = 6667.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.150901 restraints weight = 3833.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.152205 restraints weight = 2598.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.153016 restraints weight = 1981.220| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 7921 Z= 0.106 Angle : 0.577 9.733 10897 Z= 0.286 Chirality : 0.042 0.256 1336 Planarity : 0.004 0.059 1419 Dihedral : 9.326 162.288 1301 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.34 % Allowed : 26.92 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1180 helix: 1.22 (0.19), residues: 795 sheet: -1.60 (0.70), residues: 70 loop : -2.56 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 486 TYR 0.039 0.002 TYR C 263 PHE 0.039 0.001 PHE C 314 TRP 0.015 0.001 TRP C1037 HIS 0.002 0.000 HIS C1024 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7921) covalent geometry : angle 0.57712 (10897) hydrogen bonds : bond 0.03125 ( 545) hydrogen bonds : angle 3.88236 ( 1605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: C 233 MET cc_start: 0.7488 (tpp) cc_final: 0.6708 (tpp) REVERT: C 475 TYR cc_start: 0.8422 (t80) cc_final: 0.7790 (t80) REVERT: C 598 ARG cc_start: 0.7967 (ttm110) cc_final: 0.7543 (mtp85) REVERT: C 1068 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7157 (t80) REVERT: C 1190 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: C 1191 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: C 1206 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7550 (mt-10) REVERT: C 1272 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5286 (mp) REVERT: C 1305 MET cc_start: 0.8375 (tpp) cc_final: 0.7990 (tpp) outliers start: 17 outliers final: 12 residues processed: 136 average time/residue: 0.0666 time to fit residues: 13.7265 Evaluate side-chains 137 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 889 HIS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1190 GLN Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 107 optimal weight: 40.0000 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 51 optimal weight: 50.0000 chunk 105 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 57 optimal weight: 0.4980 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.154828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.135989 restraints weight = 14712.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.139053 restraints weight = 6906.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.140968 restraints weight = 4023.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.142200 restraints weight = 2758.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.142927 restraints weight = 2130.189| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 7921 Z= 0.268 Angle : 0.720 9.800 10897 Z= 0.371 Chirality : 0.049 0.329 1336 Planarity : 0.004 0.053 1419 Dihedral : 9.804 161.440 1301 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 5.70 % Allowed : 24.75 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.25), residues: 1180 helix: 0.55 (0.19), residues: 791 sheet: -2.06 (0.71), residues: 68 loop : -2.64 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1187 TYR 0.024 0.002 TYR C 263 PHE 0.039 0.002 PHE C 314 TRP 0.016 0.002 TRP C 778 HIS 0.007 0.002 HIS C1364 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 7921) covalent geometry : angle 0.71979 (10897) hydrogen bonds : bond 0.04228 ( 545) hydrogen bonds : angle 4.64221 ( 1605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 475 TYR cc_start: 0.8636 (t80) cc_final: 0.8186 (t80) REVERT: C 1068 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7103 (t80) REVERT: C 1190 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: C 1191 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: C 1219 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.6172 (t80) REVERT: C 1272 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5724 (mp) REVERT: C 1290 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6246 (mpp) outliers start: 29 outliers final: 21 residues processed: 144 average time/residue: 0.0656 time to fit residues: 14.3876 Evaluate side-chains 151 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 889 HIS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1037 TRP Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1190 GLN Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1253 GLU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1290 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 52 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 50.0000 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 98 optimal weight: 30.0000 chunk 112 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.157282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.138614 restraints weight = 14626.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.141703 restraints weight = 6789.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.143673 restraints weight = 3907.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.144922 restraints weight = 2656.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145700 restraints weight = 2041.982| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7921 Z= 0.179 Angle : 0.652 9.895 10897 Z= 0.331 Chirality : 0.045 0.268 1336 Planarity : 0.004 0.079 1419 Dihedral : 9.735 161.260 1301 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.70 % Allowed : 25.54 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.25), residues: 1180 helix: 0.65 (0.19), residues: 793 sheet: -1.51 (0.78), residues: 62 loop : -2.87 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 598 TYR 0.017 0.002 TYR C 263 PHE 0.036 0.002 PHE C 314 TRP 0.018 0.002 TRP C1037 HIS 0.004 0.001 HIS C1364 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7921) covalent geometry : angle 0.65236 (10897) hydrogen bonds : bond 0.03758 ( 545) hydrogen bonds : angle 4.39353 ( 1605) =============================================================================== Job complete usr+sys time: 1236.14 seconds wall clock time: 21 minutes 53.40 seconds (1313.40 seconds total)