Starting phenix.real_space_refine on Fri Jul 25 22:53:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pz9_20528/07_2025/6pz9_20528_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pz9_20528/07_2025/6pz9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pz9_20528/07_2025/6pz9_20528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pz9_20528/07_2025/6pz9_20528.map" model { file = "/net/cci-nas-00/data/ceres_data/6pz9_20528/07_2025/6pz9_20528_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pz9_20528/07_2025/6pz9_20528_neut.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 30, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 22, 'TRP:plan': 3, 'ASP:plan': 39, 'PHE:plan': 17, 'GLU:plan': 37, 'ARG:plan': 29} 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: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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: 5.20, per 1000 atoms: 0.67 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.92 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: 2.79 Time building geometry restraints manager: 2.88 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: 0.290 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.800 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.069 0.006 TRP C1037 HIS 0.011 0.002 HIS C1098 PHE 0.050 0.005 PHE C 432 TYR 0.040 0.004 TYR C1219 ARG 0.013 0.002 ARG C 388 Details of bonding type rmsd hydrogen bonds : bond 0.25553 ( 545) hydrogen bonds : angle 9.01541 ( 1605) covalent geometry : bond 0.00903 ( 7921) covalent geometry : angle 1.21367 (10897) *********************** 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 : 0.799 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: 0.8316 (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: 0.7855 (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: 0.5678 (mm) REVERT: C 1306 GLU cc_start: 0.7648 (tp30) cc_final: 0.7291 (tp30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1742 time to fit residues: 44.1253 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 : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4211 r_free = 0.4211 target = 0.162594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.144470 restraints weight = 14308.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.147668 restraints weight = 6588.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.149651 restraints weight = 3751.655| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7921 Z= 0.149 Angle : 0.651 10.194 10897 Z= 0.336 Chirality : 0.044 0.343 1336 Planarity : 0.005 0.061 1419 Dihedral : 10.452 152.627 1301 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.73 % Allowed : 12.38 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.23), residues: 1180 helix: -0.53 (0.18), residues: 797 sheet: -2.46 (0.62), residues: 64 loop : -3.04 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C1037 HIS 0.007 0.001 HIS C1098 PHE 0.027 0.002 PHE C 432 TYR 0.017 0.002 TYR C1219 ARG 0.007 0.001 ARG C 486 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 545) hydrogen bonds : angle 4.86795 ( 1605) covalent geometry : bond 0.00306 ( 7921) covalent geometry : angle 0.65056 (10897) *********************** 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: 19 poor density : 145 time to evaluate : 0.917 Fit side-chains REVERT: C 429 MET cc_start: 0.8406 (ttm) cc_final: 0.8161 (ttm) REVERT: C 475 TYR cc_start: 0.8363 (t80) cc_final: 0.8151 (t80) REVERT: C 770 VAL cc_start: 0.9255 (t) cc_final: 0.9014 (p) REVERT: C 852 PHE cc_start: 0.7606 (m-10) cc_final: 0.7405 (m-10) REVERT: C 1168 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.6762 (tp) outliers start: 19 outliers final: 12 residues processed: 159 average time/residue: 0.1441 time to fit residues: 34.1604 Evaluate side-chains 131 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 chunk 10 optimal weight: 0.0010 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 97 optimal weight: 50.0000 chunk 15 optimal weight: 4.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- 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** C1301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.140322 restraints weight = 14671.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143540 restraints weight = 6674.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.145591 restraints weight = 3781.016| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7921 Z= 0.185 Angle : 0.653 9.914 10897 Z= 0.334 Chirality : 0.046 0.301 1336 Planarity : 0.005 0.056 1419 Dihedral : 10.206 156.816 1301 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.89 % Allowed : 13.56 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.24), residues: 1180 helix: 0.05 (0.18), residues: 800 sheet: -2.45 (0.61), residues: 69 loop : -2.98 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C1037 HIS 0.004 0.001 HIS C1098 PHE 0.021 0.002 PHE C 321 TYR 0.016 0.002 TYR C 378 ARG 0.005 0.001 ARG C 486 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 545) hydrogen bonds : angle 4.62958 ( 1605) covalent geometry : bond 0.00398 ( 7921) covalent geometry : angle 0.65311 (10897) *********************** 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 159 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: C 253 LEU cc_start: 0.8143 (tm) cc_final: 0.7884 (tp) REVERT: C 400 MET cc_start: 0.9258 (mmm) cc_final: 0.9043 (mmp) REVERT: C 412 MET cc_start: 0.6884 (ptp) cc_final: 0.6507 (ptp) REVERT: C 424 ASP cc_start: 0.8192 (t70) cc_final: 0.7978 (t70) REVERT: C 451 LEU cc_start: 0.5547 (pp) cc_final: 0.4904 (mp) REVERT: C 1033 TRP cc_start: 0.5449 (m100) cc_final: 0.5098 (m100) REVERT: C 1168 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.6860 (tp) REVERT: C 1191 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: C 1206 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7563 (mt-10) outliers start: 30 outliers final: 20 residues processed: 151 average time/residue: 0.1507 time to fit residues: 33.7902 Evaluate side-chains 140 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 418 CYS 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 605 VAL Chi-restraints excluded: chain C residue 1027 LEU 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 1191 GLN Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 397 ASN C1301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.155372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.136809 restraints weight = 14797.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.139938 restraints weight = 6773.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.141874 restraints weight = 3857.876| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7921 Z= 0.256 Angle : 0.715 9.987 10897 Z= 0.370 Chirality : 0.048 0.298 1336 Planarity : 0.005 0.051 1419 Dihedral : 10.012 156.884 1301 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 7.86 % Allowed : 15.91 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.24), residues: 1180 helix: -0.01 (0.18), residues: 790 sheet: -2.62 (0.61), residues: 68 loop : -2.93 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C1037 HIS 0.007 0.002 HIS C 867 PHE 0.033 0.002 PHE C 321 TYR 0.019 0.002 TYR C 378 ARG 0.004 0.001 ARG C 298 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 545) hydrogen bonds : angle 4.88416 ( 1605) covalent geometry : bond 0.00546 ( 7921) covalent geometry : angle 0.71476 (10897) *********************** 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 172 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: C 233 MET cc_start: 0.7570 (tpt) cc_final: 0.7328 (tpp) REVERT: C 412 MET cc_start: 0.6848 (ptp) cc_final: 0.6446 (ptp) REVERT: C 1027 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7758 (mt) REVERT: C 1033 TRP cc_start: 0.5669 (m100) cc_final: 0.4927 (m100) REVERT: C 1168 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7210 (tp) REVERT: C 1206 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7594 (mt-10) outliers start: 40 outliers final: 35 residues processed: 158 average time/residue: 0.1556 time to fit residues: 37.6117 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 : 0.875 ------------------------------------------------------------------------------- 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 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 438 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 441 MET 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 539 TYR 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 605 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1027 LEU 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 1192 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 16 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 50.0000 chunk 104 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 81 optimal weight: 0.0050 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 113 optimal weight: 30.0000 overall best weight: 1.3200 ------------------------------------------------------------------------------- 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 C1197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.161154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.142912 restraints weight = 14317.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146084 restraints weight = 6635.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.148073 restraints weight = 3808.715| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7921 Z= 0.113 Angle : 0.577 10.032 10897 Z= 0.286 Chirality : 0.043 0.287 1336 Planarity : 0.004 0.055 1419 Dihedral : 9.599 160.521 1301 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.54 % Allowed : 21.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1180 helix: 0.64 (0.19), residues: 793 sheet: -2.27 (0.63), residues: 68 loop : -2.75 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C1037 HIS 0.005 0.001 HIS C 867 PHE 0.016 0.001 PHE C 351 TYR 0.011 0.001 TYR C 378 ARG 0.005 0.001 ARG C 598 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 545) hydrogen bonds : angle 4.20511 ( 1605) covalent geometry : bond 0.00237 ( 7921) covalent geometry : angle 0.57676 (10897) *********************** 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 144 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.904 Fit side-chains REVERT: C 253 LEU cc_start: 0.8084 (tp) cc_final: 0.7639 (tp) REVERT: C 412 MET cc_start: 0.6871 (ptp) cc_final: 0.6487 (ptp) REVERT: C 475 TYR cc_start: 0.8242 (t80) cc_final: 0.7816 (t80) REVERT: C 1027 LEU cc_start: 0.7928 (mt) cc_final: 0.7707 (mt) REVERT: C 1168 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7016 (tp) REVERT: C 1191 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8043 (mt0) outliers start: 18 outliers final: 16 residues processed: 139 average time/residue: 0.1471 time to fit residues: 31.2988 Evaluate side-chains 141 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 539 TYR Chi-restraints excluded: chain C residue 581 SER 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 1138 SER Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 98 optimal weight: 40.0000 chunk 70 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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** C1234 ASN C1301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.140730 restraints weight = 14306.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.143928 restraints weight = 6593.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145931 restraints weight = 3764.834| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7921 Z= 0.171 Angle : 0.613 9.972 10897 Z= 0.311 Chirality : 0.045 0.281 1336 Planarity : 0.004 0.050 1419 Dihedral : 9.525 159.153 1301 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 7.66 % Allowed : 20.24 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1180 helix: 0.58 (0.19), residues: 797 sheet: -2.16 (0.65), residues: 68 loop : -2.72 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C1037 HIS 0.007 0.001 HIS C 867 PHE 0.021 0.002 PHE C 321 TYR 0.022 0.002 TYR C 263 ARG 0.005 0.000 ARG C 598 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 545) hydrogen bonds : angle 4.31612 ( 1605) covalent geometry : bond 0.00367 ( 7921) covalent geometry : angle 0.61263 (10897) *********************** 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 159 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: C 253 LEU cc_start: 0.8088 (tp) cc_final: 0.7598 (tp) REVERT: C 412 MET cc_start: 0.6804 (ptp) cc_final: 0.6414 (ptp) REVERT: C 475 TYR cc_start: 0.8500 (t80) cc_final: 0.8117 (t80) REVERT: C 485 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8302 (tt0) REVERT: C 1027 LEU cc_start: 0.8029 (mt) cc_final: 0.7801 (mt) REVERT: C 1168 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7073 (tp) REVERT: C 1191 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8094 (mt0) outliers start: 39 outliers final: 32 residues processed: 147 average time/residue: 0.1325 time to fit residues: 29.8075 Evaluate side-chains 153 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 438 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 441 MET 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 539 TYR 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 770 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 889 HIS 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 1166 VAL Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1291 VAL Chi-restraints excluded: chain C residue 1296 ASN 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 49 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.158764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140190 restraints weight = 14424.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.143401 restraints weight = 6646.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145415 restraints weight = 3779.011| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7921 Z= 0.169 Angle : 0.619 10.346 10897 Z= 0.313 Chirality : 0.045 0.263 1336 Planarity : 0.004 0.050 1419 Dihedral : 9.624 160.904 1301 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 8.06 % Allowed : 19.84 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1180 helix: 0.64 (0.19), residues: 799 sheet: -2.02 (0.67), residues: 68 loop : -2.68 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C1037 HIS 0.005 0.001 HIS C 867 PHE 0.020 0.001 PHE C 321 TYR 0.025 0.002 TYR C 263 ARG 0.004 0.000 ARG C 598 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 545) hydrogen bonds : angle 4.29639 ( 1605) covalent geometry : bond 0.00368 ( 7921) covalent geometry : angle 0.61880 (10897) *********************** 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: 41 poor density : 119 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: C 412 MET cc_start: 0.6850 (ptp) cc_final: 0.6442 (ptp) REVERT: C 475 TYR cc_start: 0.8495 (t80) cc_final: 0.8083 (t80) REVERT: C 485 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8367 (tm-30) REVERT: C 1027 LEU cc_start: 0.8116 (mt) cc_final: 0.7892 (mt) REVERT: C 1033 TRP cc_start: 0.5947 (m100) cc_final: 0.5152 (m100) REVERT: C 1037 TRP cc_start: 0.5801 (m-10) cc_final: 0.4852 (m-10) REVERT: C 1168 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7198 (tp) REVERT: C 1191 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: C 1261 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8621 (tt) outliers start: 41 outliers final: 34 residues processed: 146 average time/residue: 0.1331 time to fit residues: 29.8001 Evaluate side-chains 151 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 364 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 441 MET 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 539 TYR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 889 HIS 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 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 1259 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 1296 ASN Chi-restraints excluded: chain C residue 1302 LEU Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 40.0000 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 94 optimal weight: 0.0370 chunk 54 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.159576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.140705 restraints weight = 14557.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.143970 restraints weight = 6731.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.146027 restraints weight = 3851.938| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7921 Z= 0.147 Angle : 0.599 9.850 10897 Z= 0.300 Chirality : 0.044 0.268 1336 Planarity : 0.004 0.053 1419 Dihedral : 9.538 161.335 1301 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 7.86 % Allowed : 21.02 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1180 helix: 0.81 (0.19), residues: 798 sheet: -1.84 (0.69), residues: 68 loop : -2.65 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C1037 HIS 0.004 0.001 HIS C 867 PHE 0.016 0.001 PHE C 321 TYR 0.021 0.002 TYR C 263 ARG 0.003 0.000 ARG C 486 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 545) hydrogen bonds : angle 4.16076 ( 1605) covalent geometry : bond 0.00319 ( 7921) covalent geometry : angle 0.59898 (10897) *********************** 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 158 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 412 MET cc_start: 0.6835 (ptp) cc_final: 0.6437 (ptp) REVERT: C 475 TYR cc_start: 0.8456 (t80) cc_final: 0.8068 (t80) REVERT: C 485 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 1033 TRP cc_start: 0.5833 (m100) cc_final: 0.5120 (m100) REVERT: C 1191 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: C 1261 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8633 (tt) outliers start: 40 outliers final: 32 residues processed: 144 average time/residue: 0.1380 time to fit residues: 30.5228 Evaluate side-chains 147 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 THR 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 364 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 441 MET 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 539 TYR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 605 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 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 1191 GLN Chi-restraints excluded: chain C residue 1259 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 1296 ASN Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.163151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.144428 restraints weight = 14382.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.147686 restraints weight = 6676.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.149762 restraints weight = 3803.295| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 7921 Z= 0.112 Angle : 0.567 9.729 10897 Z= 0.281 Chirality : 0.042 0.259 1336 Planarity : 0.003 0.055 1419 Dihedral : 9.387 162.979 1301 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.72 % Allowed : 24.17 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1180 helix: 1.19 (0.19), residues: 793 sheet: -1.55 (0.71), residues: 68 loop : -2.64 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C1037 HIS 0.005 0.001 HIS C 867 PHE 0.012 0.001 PHE C 351 TYR 0.017 0.001 TYR C 377 ARG 0.003 0.000 ARG C 486 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 545) hydrogen bonds : angle 3.93673 ( 1605) covalent geometry : bond 0.00247 ( 7921) covalent geometry : angle 0.56734 (10897) *********************** 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 143 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: C 260 LEU cc_start: 0.8795 (tp) cc_final: 0.8562 (tt) REVERT: C 412 MET cc_start: 0.6974 (ptp) cc_final: 0.6632 (ptp) REVERT: C 475 TYR cc_start: 0.8259 (t80) cc_final: 0.7876 (t80) REVERT: C 485 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8306 (tm-30) REVERT: C 1033 TRP cc_start: 0.5871 (m100) cc_final: 0.5333 (m100) REVERT: C 1191 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: C 1305 MET cc_start: 0.8322 (tpp) cc_final: 0.8002 (tpp) outliers start: 24 outliers final: 20 residues processed: 137 average time/residue: 0.1458 time to fit residues: 30.7693 Evaluate side-chains 134 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 539 TYR 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 1138 SER Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1291 VAL Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 113 optimal weight: 50.0000 chunk 106 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 50 optimal weight: 30.0000 chunk 59 optimal weight: 50.0000 chunk 97 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 overall best weight: 1.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 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 = 0.4212 r_free = 0.4212 target = 0.163231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.144397 restraints weight = 14347.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.147629 restraints weight = 6772.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.149701 restraints weight = 3918.031| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7921 Z= 0.117 Angle : 0.572 10.374 10897 Z= 0.282 Chirality : 0.043 0.258 1336 Planarity : 0.004 0.055 1419 Dihedral : 9.306 162.013 1301 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.32 % Allowed : 24.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1180 helix: 1.32 (0.19), residues: 794 sheet: -1.38 (0.72), residues: 68 loop : -2.60 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C1037 HIS 0.005 0.001 HIS C 867 PHE 0.048 0.001 PHE C 314 TYR 0.017 0.001 TYR C 377 ARG 0.003 0.000 ARG C 598 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 545) hydrogen bonds : angle 3.90804 ( 1605) covalent geometry : bond 0.00255 ( 7921) covalent geometry : angle 0.57230 (10897) ********************** 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 136 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.787 Fit side-chains REVERT: C 412 MET cc_start: 0.6988 (ptp) cc_final: 0.6630 (ptp) REVERT: C 475 TYR cc_start: 0.8265 (t80) cc_final: 0.7885 (t80) REVERT: C 485 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 1033 TRP cc_start: 0.5893 (m100) cc_final: 0.5377 (m100) REVERT: C 1037 TRP cc_start: 0.5685 (m-10) cc_final: 0.4934 (m-90) REVERT: C 1191 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: C 1305 MET cc_start: 0.8381 (tpp) cc_final: 0.8052 (tpp) outliers start: 22 outliers final: 21 residues processed: 130 average time/residue: 0.1386 time to fit residues: 27.9197 Evaluate side-chains 135 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 539 TYR 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 1138 SER Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1291 VAL Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 61 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.163116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144166 restraints weight = 14068.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.147450 restraints weight = 6637.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.149544 restraints weight = 3820.080| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 7921 Z= 0.111 Angle : 0.562 10.227 10897 Z= 0.277 Chirality : 0.043 0.257 1336 Planarity : 0.003 0.055 1419 Dihedral : 9.248 162.241 1301 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.32 % Allowed : 24.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1180 helix: 1.45 (0.19), residues: 794 sheet: -1.24 (0.73), residues: 68 loop : -2.54 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C1037 HIS 0.005 0.001 HIS C 867 PHE 0.042 0.001 PHE C 314 TYR 0.017 0.001 TYR C 377 ARG 0.003 0.000 ARG C 486 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 545) hydrogen bonds : angle 3.81580 ( 1605) covalent geometry : bond 0.00242 ( 7921) covalent geometry : angle 0.56227 (10897) =============================================================================== Job complete usr+sys time: 2446.60 seconds wall clock time: 43 minutes 36.07 seconds (2616.07 seconds total)