Starting phenix.real_space_refine on Fri Oct 23 16:09:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsz_65311/10_2026/9vsz_65311.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsz_65311/10_2026/9vsz_65311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vsz_65311/10_2026/9vsz_65311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsz_65311/10_2026/9vsz_65311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vsz_65311/10_2026/9vsz_65311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsz_65311/10_2026/9vsz_65311.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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 S 62 5.16 5 C 6530 2.51 5 N 1675 2.21 5 O 1836 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10105 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 10083 Classifications: {'peptide': 1263} Link IDs: {'PTRANS': 53, 'TRANS': 1209} Chain breaks: 3 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'TPF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.28, per 1000 atoms: 0.23 Number of scatterers: 10105 At special positions: 0 Unit cell: (74.27, 103.978, 146.418, 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 62 16.00 F 2 9.00 O 1836 8.00 N 1675 7.00 C 6530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 712 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1402 " - pdb=" SG CYS A1444 " distance=2.02 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1441 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 347.0 milliseconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 59.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 247 through 258 removed outlier: 3.541A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.818A pdb=" N ALA A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.826A pdb=" N ARG A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.697A pdb=" N SER A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 389 through 399 removed outlier: 4.560A pdb=" N GLU A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.653A pdb=" N ASN A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 465 removed outlier: 3.821A pdb=" N GLU A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A 463 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.612A pdb=" N ALA A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 511 Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.616A pdb=" N SER A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 542 through 559 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 563 through 581 removed outlier: 4.165A pdb=" N SER A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) Proline residue: A 573 - end of helix Processing helix chain 'A' and resid 585 through 596 Processing helix chain 'A' and resid 597 through 616 removed outlier: 3.727A pdb=" N MET A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 648 removed outlier: 3.640A pdb=" N PHE A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 670 removed outlier: 3.594A pdb=" N THR A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Proline residue: A 659 - end of helix removed outlier: 4.446A pdb=" N VAL A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 691 through 705 removed outlier: 3.727A pdb=" N TYR A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'A' and resid 762 through 784 removed outlier: 3.603A pdb=" N GLU A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 Processing helix chain 'A' and resid 932 through 936 Processing helix chain 'A' and resid 951 through 964 removed outlier: 3.627A pdb=" N SER A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 984 Processing helix chain 'A' and resid 1002 through 1016 removed outlier: 3.718A pdb=" N GLU A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1049 Processing helix chain 'A' and resid 1062 through 1067 Processing helix chain 'A' and resid 1091 through 1101 removed outlier: 3.642A pdb=" N TYR A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1121 removed outlier: 3.723A pdb=" N LEU A1117 " --> pdb=" O ALA A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1156 removed outlier: 3.633A pdb=" N GLN A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1174 through 1193 Processing helix chain 'A' and resid 1193 through 1215 removed outlier: 4.023A pdb=" N ILE A1197 " --> pdb=" O SER A1193 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR A1198 " --> pdb=" O PRO A1194 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A1199 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A1215 " --> pdb=" O ASN A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1235 removed outlier: 4.112A pdb=" N GLN A1226 " --> pdb=" O MET A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1258 Proline residue: A1248 - end of helix removed outlier: 3.651A pdb=" N GLN A1253 " --> pdb=" O TYR A1249 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1256 " --> pdb=" O LYS A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1300 removed outlier: 3.915A pdb=" N GLU A1280 " --> pdb=" O GLN A1276 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A1281 " --> pdb=" O ILE A1277 " (cutoff:3.500A) Proline residue: A1282 - end of helix removed outlier: 4.392A pdb=" N TYR A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Proline residue: A1298 - end of helix Processing helix chain 'A' and resid 1301 through 1305 Processing helix chain 'A' and resid 1310 through 1339 removed outlier: 4.363A pdb=" N PHE A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1360 removed outlier: 3.625A pdb=" N ALA A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1349 " --> pdb=" O ASN A1345 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A1360 " --> pdb=" O MET A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1380 Processing helix chain 'A' and resid 1381 through 1393 removed outlier: 3.790A pdb=" N TYR A1385 " --> pdb=" O ASN A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1422 Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.616A pdb=" N PHE A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1456 removed outlier: 4.167A pdb=" N PHE A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A1455 " --> pdb=" O THR A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1490 removed outlier: 3.576A pdb=" N VAL A1490 " --> pdb=" O TRP A1486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.510A pdb=" N THR A 216 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 236 removed outlier: 6.317A pdb=" N GLN A 324 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA A 359 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TRP A 326 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR A 183 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 384 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AA4, first strand: chain 'A' and resid 874 through 885 removed outlier: 6.275A pdb=" N TYR A 866 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP A 879 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 864 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 881 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 862 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY A 883 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N PHE A 860 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 864 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP A 919 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR A 866 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE A 917 " --> pdb=" O TYR A 866 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 937 through 940 removed outlier: 6.100A pdb=" N GLY A 938 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP A1026 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 940 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A1023 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR A1057 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU A1025 " --> pdb=" O THR A1057 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR A 891 " --> pdb=" O CYS A1056 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 890 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU A1073 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA A 892 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A1075 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N MET A 894 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU A1072 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A1084 " --> pdb=" O LEU A1072 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE A1074 " --> pdb=" O ALA A1082 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1408 through 1410 496 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2101 1.33 - 1.45: 2618 1.45 - 1.57: 5551 1.57 - 1.69: 1 1.69 - 1.82: 101 Bond restraints: 10372 Sorted by residual: bond pdb=" CZ ARG A 644 " pdb=" NH2 ARG A 644 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.22e+00 bond pdb=" N LEU A 598 " pdb=" CA LEU A 598 " ideal model delta sigma weight residual 1.461 1.487 -0.026 9.20e-03 1.18e+04 8.20e+00 bond pdb=" C3 TPF A1601 " pdb=" N2 TPF A1601 " ideal model delta sigma weight residual 1.312 1.365 -0.053 2.00e-02 2.50e+03 7.15e+00 bond pdb=" CA ILE A 514 " pdb=" C ILE A 514 " ideal model delta sigma weight residual 1.523 1.546 -0.023 9.20e-03 1.18e+04 6.08e+00 bond pdb=" N CYS A1357 " pdb=" CA CYS A1357 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.35e-02 5.49e+03 5.71e+00 ... (remaining 10367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 13203 1.51 - 3.02: 688 3.02 - 4.53: 149 4.53 - 6.04: 26 6.04 - 7.55: 6 Bond angle restraints: 14072 Sorted by residual: angle pdb=" C SER A 513 " pdb=" N ILE A 514 " pdb=" CA ILE A 514 " ideal model delta sigma weight residual 120.33 124.05 -3.72 8.00e-01 1.56e+00 2.16e+01 angle pdb=" OE1 GLN A1245 " pdb=" CD GLN A1245 " pdb=" NE2 GLN A1245 " ideal model delta sigma weight residual 122.60 118.03 4.57 1.00e+00 1.00e+00 2.09e+01 angle pdb=" C MET A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta sigma weight residual 120.00 124.23 -4.23 1.10e+00 8.26e-01 1.48e+01 angle pdb=" N GLU A1462 " pdb=" CA GLU A1462 " pdb=" C GLU A1462 " ideal model delta sigma weight residual 113.02 107.46 5.56 1.49e+00 4.50e-01 1.39e+01 angle pdb=" C ASP A 511 " pdb=" N PRO A 512 " pdb=" CA PRO A 512 " ideal model delta sigma weight residual 119.87 123.60 -3.73 1.04e+00 9.25e-01 1.29e+01 ... (remaining 14067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5417 17.86 - 35.72: 506 35.72 - 53.57: 128 53.57 - 71.43: 19 71.43 - 89.29: 12 Dihedral angle restraints: 6082 sinusoidal: 2398 harmonic: 3684 Sorted by residual: dihedral pdb=" CB CYS A 712 " pdb=" SG CYS A 712 " pdb=" SG CYS A 732 " pdb=" CB CYS A 732 " ideal model delta sinusoidal sigma weight residual -86.00 -156.87 70.87 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1441 " pdb=" CB CYS A1441 " ideal model delta sinusoidal sigma weight residual 93.00 155.10 -62.10 1 1.00e+01 1.00e-02 5.11e+01 dihedral pdb=" C ILE A1237 " pdb=" N ILE A1237 " pdb=" CA ILE A1237 " pdb=" CB ILE A1237 " ideal model delta harmonic sigma weight residual -122.00 -134.52 12.52 0 2.50e+00 1.60e-01 2.51e+01 ... (remaining 6079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1336 0.072 - 0.144: 163 0.144 - 0.217: 19 0.217 - 0.289: 3 0.289 - 0.361: 1 Chirality restraints: 1522 Sorted by residual: chirality pdb=" CA ILE A1237 " pdb=" N ILE A1237 " pdb=" C ILE A1237 " pdb=" CB ILE A1237 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA PRO A1238 " pdb=" N PRO A1238 " pdb=" C PRO A1238 " pdb=" CB PRO A1238 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL A1387 " pdb=" CA VAL A1387 " pdb=" CG1 VAL A1387 " pdb=" CG2 VAL A1387 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1519 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 552 " 0.086 2.00e-02 2.50e+03 5.37e-02 5.06e+01 pdb=" CG PHE A 552 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 552 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 PHE A 552 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE A 552 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE A 552 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 552 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1325 " 0.080 2.00e-02 2.50e+03 4.97e-02 4.32e+01 pdb=" CG PHE A1325 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A1325 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE A1325 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE A1325 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A1325 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A1325 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1374 " -0.082 2.00e-02 2.50e+03 3.99e-02 3.98e+01 pdb=" CG TRP A1374 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A1374 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A1374 " 0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP A1374 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP A1374 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1374 " 0.050 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1374 " -0.046 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1374 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A1374 " -0.042 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 302 2.71 - 3.26: 10088 3.26 - 3.81: 16866 3.81 - 4.35: 22226 4.35 - 4.90: 37065 Nonbonded interactions: 86547 Sorted by model distance: nonbonded pdb=" OG1 THR A 434 " pdb=" OE1 GLU A 437 " model vdw 2.166 3.040 nonbonded pdb=" N GLU A 948 " pdb=" OE1 GLU A 948 " model vdw 2.196 3.120 nonbonded pdb=" OH TYR A 235 " pdb=" OD2 ASP A 327 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 722 " pdb=" O TYR A1421 " model vdw 2.256 3.040 nonbonded pdb=" O TYR A 670 " pdb=" ND2 ASN A 688 " model vdw 2.257 3.120 ... (remaining 86542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.005 0.053 10375 Z= 0.269 Angle : 0.796 7.548 14078 Z= 0.510 Chirality : 0.050 0.361 1522 Planarity : 0.006 0.054 1793 Dihedral : 15.244 89.288 3717 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.39 % Allowed : 10.86 % Favored : 87.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1255 helix: 0.18 (0.19), residues: 675 sheet: -0.68 (0.51), residues: 94 loop : -1.30 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 856 TYR 0.062 0.002 TYR A 628 PHE 0.086 0.006 PHE A 552 TRP 0.082 0.003 TRP A1374 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.27 (10372) covalent geometry : angle 0.79610 / 0.51 (14072) SS BOND : bond 0.00595 / 0.29 ( 3) SS BOND : angle 1.07292 / 0.60 ( 6) hydrogen bonds : bond 0.17018 / 11.38 ( 496) hydrogen bonds : angle 6.20621 / 4.25 ( 1437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.282 Fit side-chains REVERT: A 657 MET cc_start: 0.7885 (mmm) cc_final: 0.7520 (mmm) outliers start: 15 outliers final: 11 residues processed: 120 average time/residue: 0.5424 time to fit residues: 70.2030 Evaluate side-chains 110 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1357 CYS Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain A residue 1459 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 617 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107726 restraints weight = 12822.104| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.95 r_work: 0.3106 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10375 Z= 0.157 Angle : 0.554 8.707 14078 Z= 0.291 Chirality : 0.043 0.156 1522 Planarity : 0.004 0.040 1793 Dihedral : 5.942 75.787 1414 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.51 % Allowed : 9.84 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.23), residues: 1255 helix: 0.67 (0.20), residues: 688 sheet: -0.57 (0.49), residues: 95 loop : -1.34 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 856 TYR 0.015 0.001 TYR A1460 PHE 0.024 0.002 PHE A 705 TRP 0.011 0.001 TRP A 634 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (10372) covalent geometry : angle 0.55385 / 0.29 (14072) SS BOND : bond 0.00716 / 0.35 ( 3) SS BOND : angle 0.83915 / 0.48 ( 6) hydrogen bonds : bond 0.04200 / 2.80 ( 496) hydrogen bonds : angle 4.29995 / 2.97 ( 1437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 123 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 457 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: A 461 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6495 (tt0) REVERT: A 869 LYS cc_start: 0.7782 (tppp) cc_final: 0.6584 (mppt) outliers start: 27 outliers final: 14 residues processed: 123 average time/residue: 0.5518 time to fit residues: 73.1351 Evaluate side-chains 117 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1446 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [50, 115, 48, 12, 68, 79, 0, 22, 52, 118, 82] chunk 50 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.0870 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106918 restraints weight = 12957.120| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.94 r_work: 0.3095 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10375 Z= 0.161 Angle : 0.547 9.068 14078 Z= 0.285 Chirality : 0.043 0.155 1522 Planarity : 0.004 0.043 1793 Dihedral : 5.785 75.052 1404 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.88 % Allowed : 11.14 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.23), residues: 1255 helix: 0.76 (0.19), residues: 695 sheet: -0.60 (0.49), residues: 95 loop : -1.41 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 856 TYR 0.015 0.001 TYR A1460 PHE 0.023 0.002 PHE A 705 TRP 0.011 0.001 TRP A 634 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (10372) covalent geometry : angle 0.54657 / 0.28 (14072) SS BOND : bond 0.00373 / 0.19 ( 3) SS BOND : angle 1.10542 / 0.61 ( 6) hydrogen bonds : bond 0.03981 / 2.67 ( 496) hydrogen bonds : angle 4.11748 / 2.84 ( 1437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 123 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8013 (tp) REVERT: A 126 ARG cc_start: 0.7116 (tpt90) cc_final: 0.6800 (tpt90) REVERT: A 294 ASN cc_start: 0.7979 (p0) cc_final: 0.7743 (p0) REVERT: A 457 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 461 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6404 (tt0) REVERT: A 742 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: A 869 LYS cc_start: 0.7713 (tppp) cc_final: 0.7493 (tppp) outliers start: 31 outliers final: 14 residues processed: 121 average time/residue: 0.5628 time to fit residues: 73.1968 Evaluate side-chains 117 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1114 GLU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1402 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [28, 52, 46, 113, 45, 97, 59, 60, 31, 63, 22] chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 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 = 0.3505 r_free = 0.3505 target = 0.130746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106189 restraints weight = 13054.645| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.95 r_work: 0.3084 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10375 Z= 0.179 Angle : 0.553 9.238 14078 Z= 0.286 Chirality : 0.043 0.154 1522 Planarity : 0.004 0.041 1793 Dihedral : 5.814 74.676 1404 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.97 % Allowed : 11.88 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1255 helix: 0.84 (0.20), residues: 695 sheet: -0.58 (0.50), residues: 95 loop : -1.43 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 856 TYR 0.017 0.002 TYR A1460 PHE 0.024 0.002 PHE A 705 TRP 0.010 0.001 TRP A 634 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (10372) covalent geometry : angle 0.55212 / 0.29 (14072) SS BOND : bond 0.00429 / 0.22 ( 3) SS BOND : angle 1.21156 / 0.67 ( 6) hydrogen bonds : bond 0.03953 / 2.65 ( 496) hydrogen bonds : angle 4.08301 / 2.81 ( 1437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.374 Fit side-chains REVERT: A 123 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8017 (tp) REVERT: A 126 ARG cc_start: 0.7266 (tpt90) cc_final: 0.6910 (tpt90) REVERT: A 294 ASN cc_start: 0.7925 (p0) cc_final: 0.7566 (p0) REVERT: A 331 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6154 (mmp-170) REVERT: A 457 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: A 461 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6414 (tt0) REVERT: A 742 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: A 869 LYS cc_start: 0.7742 (tppp) cc_final: 0.7452 (tppp) REVERT: A 1076 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: A 1201 ILE cc_start: 0.8397 (mm) cc_final: 0.8171 (mt) outliers start: 32 outliers final: 13 residues processed: 124 average time/residue: 0.5877 time to fit residues: 78.2940 Evaluate side-chains 119 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1114 GLU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1402 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [56, 22, 73, 26, 61, 90, 109, 114, 3, 88, 33] chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 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 = 0.3530 r_free = 0.3530 target = 0.132821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108292 restraints weight = 12888.368| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.95 r_work: 0.3111 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10375 Z= 0.126 Angle : 0.515 8.961 14078 Z= 0.264 Chirality : 0.041 0.151 1522 Planarity : 0.004 0.040 1793 Dihedral : 5.662 76.100 1404 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.79 % Allowed : 13.09 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1255 helix: 1.12 (0.20), residues: 691 sheet: -0.52 (0.51), residues: 96 loop : -1.32 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 856 TYR 0.012 0.001 TYR A1297 PHE 0.018 0.001 PHE A 552 TRP 0.010 0.001 TRP A 634 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10372) covalent geometry : angle 0.51502 / 0.26 (14072) SS BOND : bond 0.00311 / 0.16 ( 3) SS BOND : angle 1.01478 / 0.56 ( 6) hydrogen bonds : bond 0.03498 / 2.36 ( 496) hydrogen bonds : angle 3.91057 / 2.70 ( 1437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.375 Fit side-chains REVERT: A 123 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7981 (tp) REVERT: A 294 ASN cc_start: 0.7923 (p0) cc_final: 0.7518 (p0) REVERT: A 362 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: A 413 THR cc_start: 0.8279 (m) cc_final: 0.7956 (m) REVERT: A 450 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6829 (mm-30) REVERT: A 457 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 461 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6352 (tt0) REVERT: A 869 LYS cc_start: 0.7723 (tppp) cc_final: 0.7406 (tppp) REVERT: A 1076 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: A 1201 ILE cc_start: 0.8411 (mm) cc_final: 0.8150 (mt) outliers start: 30 outliers final: 12 residues processed: 125 average time/residue: 0.5664 time to fit residues: 76.2886 Evaluate side-chains 120 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1114 GLU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1402 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [60, 71, 85, 40, 118, 84, 78, 108, 46, 70, 16] chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 78 optimal weight: 0.0670 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106923 restraints weight = 13037.096| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.96 r_work: 0.3092 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10375 Z= 0.169 Angle : 0.545 9.168 14078 Z= 0.280 Chirality : 0.043 0.152 1522 Planarity : 0.004 0.041 1793 Dihedral : 5.632 75.039 1403 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.25 % Allowed : 12.26 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.23), residues: 1255 helix: 1.08 (0.20), residues: 691 sheet: -0.52 (0.51), residues: 96 loop : -1.32 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1436 TYR 0.015 0.001 TYR A1297 PHE 0.022 0.002 PHE A 705 TRP 0.009 0.001 TRP A 634 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (10372) covalent geometry : angle 0.54468 / 0.28 (14072) SS BOND : bond 0.00409 / 0.21 ( 3) SS BOND : angle 1.19749 / 0.66 ( 6) hydrogen bonds : bond 0.03733 / 2.51 ( 496) hydrogen bonds : angle 3.98638 / 2.74 ( 1437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.328 Fit side-chains REVERT: A 123 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8042 (tp) REVERT: A 126 ARG cc_start: 0.7247 (tpt90) cc_final: 0.6930 (tpt90) REVERT: A 294 ASN cc_start: 0.7907 (p0) cc_final: 0.7541 (p0) REVERT: A 331 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6096 (mmp-170) REVERT: A 413 THR cc_start: 0.8274 (m) cc_final: 0.7941 (m) REVERT: A 450 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6814 (mm-30) REVERT: A 457 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 461 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6247 (tt0) REVERT: A 742 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: A 1076 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: A 1201 ILE cc_start: 0.8454 (mm) cc_final: 0.8173 (mt) outliers start: 35 outliers final: 18 residues processed: 126 average time/residue: 0.5785 time to fit residues: 78.5252 Evaluate side-chains 125 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1114 GLU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [68, 54, 33, 14, 100, 55, 73, 95, 117, 102, 108] chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 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 = 0.3498 r_free = 0.3498 target = 0.130143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105645 restraints weight = 12940.597| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.94 r_work: 0.3076 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10375 Z= 0.208 Angle : 0.580 9.347 14078 Z= 0.298 Chirality : 0.044 0.152 1522 Planarity : 0.004 0.043 1793 Dihedral : 5.742 73.702 1403 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.06 % Allowed : 12.72 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1255 helix: 0.95 (0.19), residues: 692 sheet: -0.56 (0.51), residues: 95 loop : -1.35 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1436 TYR 0.019 0.002 TYR A1297 PHE 0.025 0.002 PHE A 552 TRP 0.009 0.001 TRP A 634 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (10372) covalent geometry : angle 0.57945 / 0.30 (14072) SS BOND : bond 0.00515 / 0.27 ( 3) SS BOND : angle 1.37050 / 0.76 ( 6) hydrogen bonds : bond 0.04034 / 2.71 ( 496) hydrogen bonds : angle 4.10202 / 2.81 ( 1437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.355 Fit side-chains REVERT: A 123 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8026 (tp) REVERT: A 294 ASN cc_start: 0.7859 (p0) cc_final: 0.7487 (p0) REVERT: A 331 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6105 (mmp-170) REVERT: A 413 THR cc_start: 0.8185 (m) cc_final: 0.7856 (m) REVERT: A 450 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6782 (mm-30) REVERT: A 457 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 461 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6257 (tt0) REVERT: A 742 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7257 (mm-30) REVERT: A 869 LYS cc_start: 0.7661 (tppp) cc_final: 0.6374 (mppt) REVERT: A 948 GLU cc_start: 0.8216 (mp0) cc_final: 0.7912 (mt-10) REVERT: A 1076 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: A 1201 ILE cc_start: 0.8414 (mm) cc_final: 0.8146 (mt) outliers start: 33 outliers final: 19 residues processed: 126 average time/residue: 0.5795 time to fit residues: 78.5326 Evaluate side-chains 127 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1114 GLU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [28, 117, 119, 107, 56, 73, 42, 49, 98, 112, 48] chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 119 optimal weight: 0.0870 chunk 107 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 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 = 0.3529 r_free = 0.3529 target = 0.132640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108102 restraints weight = 12904.523| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.96 r_work: 0.3110 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10375 Z= 0.130 Angle : 0.523 8.996 14078 Z= 0.267 Chirality : 0.042 0.150 1522 Planarity : 0.004 0.041 1793 Dihedral : 5.568 75.240 1403 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.41 % Allowed : 13.46 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1255 helix: 1.19 (0.20), residues: 692 sheet: -0.48 (0.51), residues: 96 loop : -1.25 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1436 TYR 0.012 0.001 TYR A1297 PHE 0.021 0.001 PHE A 552 TRP 0.010 0.001 TRP A 634 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10372) covalent geometry : angle 0.52231 / 0.27 (14072) SS BOND : bond 0.00301 / 0.15 ( 3) SS BOND : angle 1.07698 / 0.59 ( 6) hydrogen bonds : bond 0.03478 / 2.34 ( 496) hydrogen bonds : angle 3.91874 / 2.69 ( 1437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.376 Fit side-chains REVERT: A 123 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7964 (tp) REVERT: A 126 ARG cc_start: 0.7265 (tpt90) cc_final: 0.6997 (tpt90) REVERT: A 294 ASN cc_start: 0.7837 (p0) cc_final: 0.7467 (p0) REVERT: A 331 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6095 (mmp-170) REVERT: A 413 THR cc_start: 0.8110 (m) cc_final: 0.7806 (m) REVERT: A 450 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6777 (mm-30) REVERT: A 457 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: A 461 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6098 (tt0) REVERT: A 742 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: A 948 GLU cc_start: 0.8056 (mp0) cc_final: 0.7841 (mt-10) REVERT: A 1076 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: A 1201 ILE cc_start: 0.8407 (mm) cc_final: 0.8133 (mt) outliers start: 26 outliers final: 16 residues processed: 122 average time/residue: 0.5748 time to fit residues: 75.1988 Evaluate side-chains 122 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1114 GLU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1402 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [95, 3, 122, 9, 82, 37, 79, 111, 53, 115, 113] chunk 95 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 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 = 0.3526 r_free = 0.3526 target = 0.132457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108005 restraints weight = 12941.572| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.96 r_work: 0.3107 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10375 Z= 0.138 Angle : 0.539 9.020 14078 Z= 0.276 Chirality : 0.042 0.216 1522 Planarity : 0.004 0.058 1793 Dihedral : 5.538 75.176 1403 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.69 % Allowed : 13.46 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1255 helix: 1.22 (0.20), residues: 692 sheet: -0.52 (0.51), residues: 96 loop : -1.22 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1436 TYR 0.013 0.001 TYR A1297 PHE 0.022 0.002 PHE A 552 TRP 0.009 0.001 TRP A 634 HIS 0.002 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10372) covalent geometry : angle 0.53873 / 0.28 (14072) SS BOND : bond 0.00328 / 0.17 ( 3) SS BOND : angle 1.10656 / 0.61 ( 6) hydrogen bonds : bond 0.03496 / 2.36 ( 496) hydrogen bonds : angle 3.91436 / 2.69 ( 1437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.301 Fit side-chains REVERT: A 123 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8051 (tp) REVERT: A 126 ARG cc_start: 0.7216 (tpt90) cc_final: 0.6937 (tpt90) REVERT: A 294 ASN cc_start: 0.7933 (p0) cc_final: 0.7569 (p0) REVERT: A 331 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6143 (mmp-170) REVERT: A 413 THR cc_start: 0.8150 (m) cc_final: 0.7831 (m) REVERT: A 450 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6810 (mm-30) REVERT: A 461 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6170 (tt0) REVERT: A 653 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6570 (mt) REVERT: A 742 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: A 869 LYS cc_start: 0.7654 (tppp) cc_final: 0.6520 (mppt) REVERT: A 948 GLU cc_start: 0.8077 (mp0) cc_final: 0.7855 (mt-10) REVERT: A 1076 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: A 1201 ILE cc_start: 0.8444 (mm) cc_final: 0.8162 (mt) outliers start: 29 outliers final: 18 residues processed: 122 average time/residue: 0.5958 time to fit residues: 78.0827 Evaluate side-chains 124 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1114 GLU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1402 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [53, 56, 75, 36, 18, 117, 12, 49, 74, 15, 40] chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104493 restraints weight = 12824.448| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.92 r_work: 0.3060 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10375 Z= 0.282 Angle : 0.641 9.557 14078 Z= 0.330 Chirality : 0.048 0.197 1522 Planarity : 0.005 0.073 1793 Dihedral : 5.838 71.879 1403 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.32 % Allowed : 14.02 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1255 helix: 0.81 (0.19), residues: 692 sheet: -0.63 (0.50), residues: 95 loop : -1.34 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1436 TYR 0.022 0.002 TYR A1297 PHE 0.031 0.003 PHE A 552 TRP 0.007 0.002 TRP A 884 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.28 (10372) covalent geometry : angle 0.64059 / 0.33 (14072) SS BOND : bond 0.00671 / 0.35 ( 3) SS BOND : angle 1.52904 / 0.85 ( 6) hydrogen bonds : bond 0.04396 / 2.95 ( 496) hydrogen bonds : angle 4.24771 / 2.90 ( 1437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.374 Fit side-chains REVERT: A 123 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8090 (tp) REVERT: A 126 ARG cc_start: 0.7234 (tpt90) cc_final: 0.6959 (tpt90) REVERT: A 226 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: A 294 ASN cc_start: 0.7934 (p0) cc_final: 0.7553 (p0) REVERT: A 331 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6211 (mmp-170) REVERT: A 461 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6266 (tt0) REVERT: A 653 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6658 (mt) REVERT: A 869 LYS cc_start: 0.7796 (tppp) cc_final: 0.6609 (mppt) REVERT: A 948 GLU cc_start: 0.8144 (mp0) cc_final: 0.7894 (mt-10) REVERT: A 1076 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: A 1201 ILE cc_start: 0.8450 (mm) cc_final: 0.8188 (mt) outliers start: 25 outliers final: 16 residues processed: 118 average time/residue: 0.5911 time to fit residues: 74.9904 Evaluate side-chains 119 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1114 GLU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1402 CYS Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: [99, 51, 46, 37, 20, 119, 44, 40, 58, 101, 13] chunk 99 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 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 = 0.3516 r_free = 0.3516 target = 0.131608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107038 restraints weight = 12899.620| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.95 r_work: 0.3094 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10375 Z= 0.144 Angle : 0.550 9.144 14078 Z= 0.283 Chirality : 0.043 0.189 1522 Planarity : 0.004 0.078 1793 Dihedral : 5.680 73.794 1403 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.04 % Allowed : 14.21 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1255 helix: 1.09 (0.20), residues: 689 sheet: -0.57 (0.50), residues: 96 loop : -1.27 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1436 TYR 0.015 0.001 TYR A1297 PHE 0.024 0.002 PHE A 552 TRP 0.010 0.001 TRP A 634 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (10372) covalent geometry : angle 0.55004 / 0.28 (14072) SS BOND : bond 0.00349 / 0.18 ( 3) SS BOND : angle 1.17377 / 0.64 ( 6) hydrogen bonds : bond 0.03657 / 2.46 ( 496) hydrogen bonds : angle 4.02249 / 2.75 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2958.59 seconds wall clock time: 51 minutes 17.56 seconds (3077.56 seconds total)