Starting phenix.real_space_refine on Thu Jul 2 18:31:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vlu_32027/07_2026/7vlu_32027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vlu_32027/07_2026/7vlu_32027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vlu_32027/07_2026/7vlu_32027.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vlu_32027/07_2026/7vlu_32027.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vlu_32027/07_2026/7vlu_32027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vlu_32027/07_2026/7vlu_32027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vlu_32027/07_2026/7vlu_32027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vlu_32027/07_2026/7vlu_32027.map" } resolution = 3.3 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= 0.019 sd= 0.147 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 5909 2.51 5 N 1507 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9110 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8998 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 34, 'TRANS': 1124} Chain breaks: 6 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 6, 'TYR:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'ESV': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.65, per 1000 atoms: 0.18 Number of scatterers: 9110 At special positions: 0 Unit cell: (74.898, 90.666, 136.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 5 15.00 Mg 2 11.99 O 1639 8.00 N 1507 7.00 C 5909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 228.7 milliseconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 70.9% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 230 through 241 removed outlier: 4.403A pdb=" N LEU A 234 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N HIS A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 278 removed outlier: 3.765A pdb=" N LYS A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 312 removed outlier: 6.376A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'A' and resid 347 through 393 Processing helix chain 'A' and resid 396 through 402 removed outlier: 4.220A pdb=" N LEU A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 428 removed outlier: 4.683A pdb=" N THR A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 451 through 462 removed outlier: 4.084A pdb=" N VAL A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 498 Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 507 through 557 Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 564 through 584 Proline residue: A 581 - end of helix removed outlier: 4.207A pdb=" N LEU A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 607 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 786 through 791 removed outlier: 3.600A pdb=" N ASP A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 839 through 850 Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.989A pdb=" N ASP A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 875 removed outlier: 3.985A pdb=" N THR A 873 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 899 through 910 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 987 through 1018 removed outlier: 4.031A pdb=" N PHE A 991 " --> pdb=" O PHE A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1074 removed outlier: 3.558A pdb=" N THR A1052 " --> pdb=" O VAL A1048 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A1053 " --> pdb=" O THR A1049 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.633A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1102 removed outlier: 4.083A pdb=" N ILE A1088 " --> pdb=" O PRO A1084 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1176 removed outlier: 4.002A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.922A pdb=" N LYS A1154 " --> pdb=" O ARG A1150 " (cutoff:3.500A) Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1177 through 1184 Processing helix chain 'A' and resid 1186 through 1236 Processing helix chain 'A' and resid 1242 through 1281 removed outlier: 3.513A pdb=" N LEU A1248 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A1253 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A1281 " --> pdb=" O LYS A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1284 No H-bonds generated for 'chain 'A' and resid 1282 through 1284' Processing helix chain 'A' and resid 1347 through 1355 Processing helix chain 'A' and resid 1377 through 1382 Processing helix chain 'A' and resid 1399 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1432 through 1435 removed outlier: 3.771A pdb=" N ASP A1435 " --> pdb=" O GLY A1432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1432 through 1435' Processing helix chain 'A' and resid 1439 through 1443 removed outlier: 3.627A pdb=" N GLU A1443 " --> pdb=" O GLU A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1461 removed outlier: 4.044A pdb=" N ARG A1461 " --> pdb=" O ARG A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1491 Processing helix chain 'A' and resid 1525 through 1532 Processing helix chain 'A' and resid 1535 through 1543 Processing sheet with id=AA1, first strand: chain 'A' and resid 687 through 692 removed outlier: 6.628A pdb=" N ILE A 687 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR A 671 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 689 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS A 669 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 691 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 748 through 751 removed outlier: 6.591A pdb=" N VAL A 829 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 865 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 831 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR A 697 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 888 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS A 882 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1331 removed outlier: 6.680A pdb=" N LYS A1326 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS A1314 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL A1328 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE A1310 " --> pdb=" O VAL A1367 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1367 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP A1312 " --> pdb=" O LYS A1365 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A1365 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A1363 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ARG A1316 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE A1361 " --> pdb=" O ARG A1316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1386 through 1388 removed outlier: 6.608A pdb=" N SER A1386 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASP A1469 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE A1388 " --> pdb=" O ASP A1469 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A1466 " --> pdb=" O VAL A1497 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE A1499 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N MET A1468 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY A1339 " --> pdb=" O LEU A1513 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A1515 " --> pdb=" O GLY A1339 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS A1341 " --> pdb=" O PHE A1515 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A1514 " --> pdb=" O GLU A1522 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A1522 " --> pdb=" O VAL A1514 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER A1516 " --> pdb=" O LEU A1520 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU A1520 " --> pdb=" O SER A1516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1397 through 1398 614 hydrogen bonds defined for protein. 1809 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: 1.12 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1428 1.27 - 1.41: 2237 1.41 - 1.54: 5530 1.54 - 1.68: 21 1.68 - 1.81: 77 Bond restraints: 9293 Sorted by residual: bond pdb=" C17 ESV A1606 " pdb=" N3 ESV A1606 " ideal model delta sigma weight residual 1.323 1.460 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" CAY Y01 A1601 " pdb=" OAW Y01 A1601 " ideal model delta sigma weight residual 1.332 1.462 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C11 ESV A1606 " pdb=" N2 ESV A1606 " ideal model delta sigma weight residual 1.380 1.468 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CAX Y01 A1601 " pdb=" OAH Y01 A1601 " ideal model delta sigma weight residual 1.248 1.331 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C12 ESV A1606 " pdb=" N2 ESV A1606 " ideal model delta sigma weight residual 1.402 1.462 -0.060 2.00e-02 2.50e+03 8.86e+00 ... (remaining 9288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 12552 2.99 - 5.97: 72 5.97 - 8.96: 10 8.96 - 11.95: 1 11.95 - 14.94: 1 Bond angle restraints: 12636 Sorted by residual: angle pdb=" N2 ESV A1606 " pdb=" C11 ESV A1606 " pdb=" N3 ESV A1606 " ideal model delta sigma weight residual 112.24 127.18 -14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" N1 ESV A1606 " pdb=" C11 ESV A1606 " pdb=" N2 ESV A1606 " ideal model delta sigma weight residual 120.75 110.72 10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C3' ATP A1605 " pdb=" C4' ATP A1605 " pdb=" C5' ATP A1605 " ideal model delta sigma weight residual 115.19 109.95 5.24 1.76e+00 3.23e-01 8.87e+00 angle pdb=" C1' ATP A1605 " pdb=" C2' ATP A1605 " pdb=" C3' ATP A1605 " ideal model delta sigma weight residual 101.56 105.01 -3.45 1.19e+00 7.05e-01 8.40e+00 angle pdb=" C4' ATP A1605 " pdb=" C3' ATP A1605 " pdb=" O3' ATP A1605 " ideal model delta sigma weight residual 111.06 104.03 7.03 2.50e+00 1.60e-01 7.91e+00 ... (remaining 12631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 5314 28.13 - 56.25: 159 56.25 - 84.38: 13 84.38 - 112.50: 0 112.50 - 140.62: 1 Dihedral angle restraints: 5487 sinusoidal: 2119 harmonic: 3368 Sorted by residual: dihedral pdb=" O2A ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PA ADP A1602 " pdb=" PB ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 80.63 -140.62 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" N GLU A 417 " pdb=" CA GLU A 417 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" O1B ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PB ADP A1602 " pdb=" PA ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 0.67 -60.67 1 2.00e+01 2.50e-03 1.22e+01 ... (remaining 5484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1315 0.057 - 0.114: 167 0.114 - 0.171: 26 0.171 - 0.228: 2 0.228 - 0.285: 3 Chirality restraints: 1513 Sorted by residual: chirality pdb=" C3' ATP A1605 " pdb=" C2' ATP A1605 " pdb=" C4' ATP A1605 " pdb=" O3' ATP A1605 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C4' ATP A1605 " pdb=" C3' ATP A1605 " pdb=" C5' ATP A1605 " pdb=" O4' ATP A1605 " both_signs ideal model delta sigma weight residual False -2.49 -2.77 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CBB Y01 A1601 " pdb=" CAC Y01 A1601 " pdb=" CAO Y01 A1601 " pdb=" CBE Y01 A1601 " both_signs ideal model delta sigma weight residual False 2.58 2.33 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1510 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A1136 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO A1137 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A1137 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1137 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 543 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO A 544 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 544 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 544 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1091 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ARG A1091 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG A1091 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE A1092 " -0.011 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 16 2.56 - 3.15: 7854 3.15 - 3.73: 14325 3.73 - 4.32: 20176 4.32 - 4.90: 33684 Nonbonded interactions: 76055 Sorted by model distance: nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A1603 " model vdw 1.978 2.170 nonbonded pdb=" CD GLN A 753 " pdb="MG MG A1603 " model vdw 2.285 2.400 nonbonded pdb=" O2' ATP A1605 " pdb=" O3' ATP A1605 " model vdw 2.344 2.432 nonbonded pdb=" O1B ADP A1602 " pdb="MG MG A1604 " model vdw 2.418 2.170 nonbonded pdb=" O ILE A 577 " pdb=" OG1 THR A 580 " model vdw 2.420 3.040 ... (remaining 76050 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: 0.530 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 9293 Z= 0.196 Angle : 0.635 14.936 12636 Z= 0.316 Chirality : 0.041 0.285 1513 Planarity : 0.004 0.054 1541 Dihedral : 12.853 140.625 3305 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.96 % Allowed : 6.09 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.35 (0.23), residues: 1145 helix: 0.23 (0.18), residues: 747 sheet: -1.10 (0.53), residues: 63 loop : -0.85 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 820 TYR 0.008 0.001 TYR A1257 PHE 0.010 0.001 PHE A 424 TRP 0.008 0.001 TRP A 230 HIS 0.006 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.20 ( 9293) covalent geometry : angle 0.63454 / 0.32 (12636) hydrogen bonds : bond 0.12127 / 7.66 ( 614) hydrogen bonds : angle 6.24764 / 4.54 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.252 Fit side-chains REVERT: A 230 TRP cc_start: 0.6144 (OUTLIER) cc_final: 0.5614 (p-90) REVERT: A 520 MET cc_start: 0.8581 (mmt) cc_final: 0.8367 (mmm) REVERT: A 987 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7946 (t80) REVERT: A 1192 GLN cc_start: 0.8171 (tt0) cc_final: 0.7900 (mt0) REVERT: A 1272 MET cc_start: 0.8512 (mmt) cc_final: 0.8301 (mmm) REVERT: A 1468 MET cc_start: 0.8876 (mtt) cc_final: 0.8591 (mtp) REVERT: A 1498 THR cc_start: 0.8285 (p) cc_final: 0.8055 (p) outliers start: 19 outliers final: 6 residues processed: 158 average time/residue: 0.0846 time to fit residues: 18.1632 Evaluate side-chains 75 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1379 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 HIS A1444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100606 restraints weight = 13205.619| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.13 r_work: 0.3160 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9293 Z= 0.189 Angle : 0.623 10.097 12636 Z= 0.311 Chirality : 0.043 0.276 1513 Planarity : 0.004 0.060 1541 Dihedral : 7.676 146.840 1277 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.48 % Allowed : 10.01 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1145 helix: 1.35 (0.18), residues: 765 sheet: -0.58 (0.55), residues: 69 loop : -0.63 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 304 TYR 0.016 0.001 TYR A1126 PHE 0.015 0.001 PHE A1207 TRP 0.009 0.001 TRP A1260 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 9293) covalent geometry : angle 0.62277 / 0.31 (12636) hydrogen bonds : bond 0.05891 / 4.02 ( 614) hydrogen bonds : angle 4.57038 / 3.42 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.412 Fit side-chains REVERT: A 243 ILE cc_start: 0.8189 (mt) cc_final: 0.7893 (mp) REVERT: A 539 MET cc_start: 0.7984 (mmm) cc_final: 0.7287 (mmm) REVERT: A 764 GLU cc_start: 0.7780 (tp30) cc_final: 0.7198 (tp30) REVERT: A 1108 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 1192 GLN cc_start: 0.7794 (tt0) cc_final: 0.7421 (mt0) REVERT: A 1272 MET cc_start: 0.8396 (mmt) cc_final: 0.8089 (mmm) REVERT: A 1398 SER cc_start: 0.8510 (m) cc_final: 0.8082 (p) REVERT: A 1468 MET cc_start: 0.8348 (mtt) cc_final: 0.7960 (mtp) outliers start: 24 outliers final: 11 residues processed: 97 average time/residue: 0.0881 time to fit residues: 12.7556 Evaluate side-chains 74 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1444 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 105 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 719 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 = 0.3603 r_free = 0.3603 target = 0.125459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103384 restraints weight = 12914.365| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.09 r_work: 0.3207 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9293 Z= 0.128 Angle : 0.533 7.970 12636 Z= 0.265 Chirality : 0.039 0.241 1513 Planarity : 0.004 0.057 1541 Dihedral : 7.093 140.727 1269 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.48 % Allowed : 11.04 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.24), residues: 1145 helix: 2.17 (0.18), residues: 759 sheet: -0.24 (0.57), residues: 69 loop : -0.42 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1382 TYR 0.009 0.001 TYR A1205 PHE 0.013 0.001 PHE A1445 TRP 0.006 0.001 TRP A 980 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9293) covalent geometry : angle 0.53272 / 0.26 (12636) hydrogen bonds : bond 0.05273 / 3.59 ( 614) hydrogen bonds : angle 4.17237 / 3.13 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.308 Fit side-chains REVERT: A 230 TRP cc_start: 0.5963 (OUTLIER) cc_final: 0.5592 (p-90) REVERT: A 243 ILE cc_start: 0.8356 (mt) cc_final: 0.8129 (mt) REVERT: A 323 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7239 (tt0) REVERT: A 405 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8170 (ptp) REVERT: A 1108 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 1192 GLN cc_start: 0.7673 (tt0) cc_final: 0.7391 (mt0) REVERT: A 1254 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7596 (tt) REVERT: A 1272 MET cc_start: 0.8233 (mmt) cc_final: 0.7893 (mmm) REVERT: A 1398 SER cc_start: 0.8598 (m) cc_final: 0.8073 (p) REVERT: A 1468 MET cc_start: 0.8416 (mtt) cc_final: 0.7966 (mtp) outliers start: 24 outliers final: 9 residues processed: 92 average time/residue: 0.0810 time to fit residues: 11.3740 Evaluate side-chains 78 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102072 restraints weight = 13213.932| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.14 r_work: 0.3178 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9293 Z= 0.145 Angle : 0.524 8.663 12636 Z= 0.260 Chirality : 0.040 0.231 1513 Planarity : 0.004 0.052 1541 Dihedral : 6.921 140.701 1268 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.27 % Allowed : 11.76 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.25), residues: 1145 helix: 2.31 (0.18), residues: 759 sheet: 0.22 (0.61), residues: 69 loop : -0.27 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1382 TYR 0.010 0.001 TYR A1205 PHE 0.011 0.001 PHE A1207 TRP 0.006 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9293) covalent geometry : angle 0.52441 / 0.26 (12636) hydrogen bonds : bond 0.05252 / 3.59 ( 614) hydrogen bonds : angle 4.10351 / 3.08 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.351 Fit side-chains REVERT: A 230 TRP cc_start: 0.5532 (OUTLIER) cc_final: 0.5095 (p-90) REVERT: A 243 ILE cc_start: 0.8427 (mt) cc_final: 0.8223 (mt) REVERT: A 405 MET cc_start: 0.8582 (ptp) cc_final: 0.8172 (ptp) REVERT: A 539 MET cc_start: 0.7436 (mmm) cc_final: 0.7163 (mmt) REVERT: A 1192 GLN cc_start: 0.7627 (tt0) cc_final: 0.7328 (mt0) REVERT: A 1254 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7490 (tt) REVERT: A 1272 MET cc_start: 0.8218 (mmt) cc_final: 0.7902 (mmm) REVERT: A 1398 SER cc_start: 0.8638 (m) cc_final: 0.8055 (p) REVERT: A 1434 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8143 (tp) REVERT: A 1468 MET cc_start: 0.8376 (mtt) cc_final: 0.7964 (mtp) outliers start: 22 outliers final: 13 residues processed: 89 average time/residue: 0.0753 time to fit residues: 10.5155 Evaluate side-chains 76 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 91 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 719 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 = 0.3600 r_free = 0.3600 target = 0.125142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.102453 restraints weight = 13131.639| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.20 r_work: 0.3172 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9293 Z= 0.138 Angle : 0.511 8.990 12636 Z= 0.254 Chirality : 0.039 0.235 1513 Planarity : 0.004 0.046 1541 Dihedral : 6.777 139.264 1267 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.89 % Allowed : 12.59 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.25), residues: 1145 helix: 2.43 (0.18), residues: 759 sheet: 0.53 (0.62), residues: 69 loop : -0.17 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1382 TYR 0.010 0.001 TYR A1205 PHE 0.011 0.001 PHE A1207 TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9293) covalent geometry : angle 0.51103 / 0.25 (12636) hydrogen bonds : bond 0.05117 / 3.51 ( 614) hydrogen bonds : angle 4.00363 / 3.00 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.351 Fit side-chains REVERT: A 230 TRP cc_start: 0.5770 (OUTLIER) cc_final: 0.5369 (p-90) REVERT: A 243 ILE cc_start: 0.8483 (mt) cc_final: 0.8275 (mt) REVERT: A 405 MET cc_start: 0.8538 (ptp) cc_final: 0.8138 (ptp) REVERT: A 539 MET cc_start: 0.7431 (mmm) cc_final: 0.7205 (mmt) REVERT: A 833 ASP cc_start: 0.8314 (t0) cc_final: 0.7049 (t70) REVERT: A 1192 GLN cc_start: 0.7628 (tt0) cc_final: 0.7283 (mt0) REVERT: A 1254 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7463 (tt) REVERT: A 1272 MET cc_start: 0.8282 (mmt) cc_final: 0.7936 (mmm) REVERT: A 1398 SER cc_start: 0.8702 (m) cc_final: 0.8104 (p) REVERT: A 1434 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 1468 MET cc_start: 0.8243 (mtt) cc_final: 0.7797 (mtp) outliers start: 28 outliers final: 19 residues processed: 93 average time/residue: 0.0743 time to fit residues: 10.8192 Evaluate side-chains 83 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1389 LEU Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 719 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 = 0.3571 r_free = 0.3571 target = 0.122975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100547 restraints weight = 13370.857| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.15 r_work: 0.3153 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9293 Z= 0.157 Angle : 0.532 9.184 12636 Z= 0.263 Chirality : 0.040 0.227 1513 Planarity : 0.004 0.043 1541 Dihedral : 6.667 139.966 1265 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.89 % Allowed : 12.69 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.25), residues: 1145 helix: 2.40 (0.18), residues: 759 sheet: 0.78 (0.64), residues: 69 loop : -0.10 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1382 TYR 0.014 0.001 TYR A1205 PHE 0.011 0.001 PHE A1207 TRP 0.007 0.001 TRP A 979 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 9293) covalent geometry : angle 0.53196 / 0.26 (12636) hydrogen bonds : bond 0.05285 / 3.62 ( 614) hydrogen bonds : angle 4.03574 / 3.02 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.355 Fit side-chains REVERT: A 270 GLU cc_start: 0.8488 (tp30) cc_final: 0.7911 (mt-10) REVERT: A 405 MET cc_start: 0.8506 (ptp) cc_final: 0.8101 (ptp) REVERT: A 422 MET cc_start: 0.7477 (ttp) cc_final: 0.7224 (ttm) REVERT: A 1154 LYS cc_start: 0.7557 (mmtp) cc_final: 0.7261 (pttp) REVERT: A 1192 GLN cc_start: 0.7678 (tt0) cc_final: 0.7279 (mt0) REVERT: A 1254 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7523 (tt) REVERT: A 1263 ARG cc_start: 0.7402 (tpp-160) cc_final: 0.7094 (tpp-160) REVERT: A 1272 MET cc_start: 0.8208 (mmt) cc_final: 0.7873 (mmm) REVERT: A 1434 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8075 (tp) REVERT: A 1468 MET cc_start: 0.8259 (mtt) cc_final: 0.7840 (mtp) outliers start: 28 outliers final: 19 residues processed: 92 average time/residue: 0.0808 time to fit residues: 11.2884 Evaluate side-chains 83 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 106 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 719 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.101931 restraints weight = 13327.899| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.16 r_work: 0.3167 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9293 Z= 0.131 Angle : 0.511 9.196 12636 Z= 0.253 Chirality : 0.039 0.232 1513 Planarity : 0.004 0.041 1541 Dihedral : 6.597 138.238 1265 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.37 % Allowed : 13.31 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.25), residues: 1145 helix: 2.48 (0.18), residues: 759 sheet: 0.81 (0.65), residues: 69 loop : -0.05 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1382 TYR 0.012 0.001 TYR A1126 PHE 0.008 0.001 PHE A1190 TRP 0.020 0.001 TRP A 230 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9293) covalent geometry : angle 0.51111 / 0.25 (12636) hydrogen bonds : bond 0.05116 / 3.51 ( 614) hydrogen bonds : angle 3.95912 / 2.96 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.262 Fit side-chains REVERT: A 270 GLU cc_start: 0.8477 (tp30) cc_final: 0.7914 (mt-10) REVERT: A 405 MET cc_start: 0.8451 (ptp) cc_final: 0.8098 (ptp) REVERT: A 1154 LYS cc_start: 0.7579 (mmtp) cc_final: 0.7301 (pttp) REVERT: A 1192 GLN cc_start: 0.7529 (tt0) cc_final: 0.7121 (mt0) REVERT: A 1263 ARG cc_start: 0.7333 (tpp-160) cc_final: 0.7030 (tpp-160) REVERT: A 1272 MET cc_start: 0.8169 (mmt) cc_final: 0.7815 (mmm) REVERT: A 1434 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8057 (tp) REVERT: A 1468 MET cc_start: 0.8224 (mtt) cc_final: 0.7811 (mtp) outliers start: 23 outliers final: 18 residues processed: 84 average time/residue: 0.0844 time to fit residues: 10.6229 Evaluate side-chains 82 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 82 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.122141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099727 restraints weight = 13314.810| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.16 r_work: 0.3143 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9293 Z= 0.169 Angle : 0.540 9.092 12636 Z= 0.267 Chirality : 0.040 0.222 1513 Planarity : 0.004 0.040 1541 Dihedral : 6.640 138.679 1265 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.48 % Allowed : 13.52 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.25), residues: 1145 helix: 2.37 (0.18), residues: 759 sheet: 0.82 (0.64), residues: 69 loop : -0.04 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1382 TYR 0.011 0.001 TYR A1126 PHE 0.014 0.001 PHE A1207 TRP 0.007 0.001 TRP A 980 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 9293) covalent geometry : angle 0.54002 / 0.27 (12636) hydrogen bonds : bond 0.05337 / 3.67 ( 614) hydrogen bonds : angle 4.04346 / 3.03 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.353 Fit side-chains REVERT: A 270 GLU cc_start: 0.8476 (tp30) cc_final: 0.7906 (mt-10) REVERT: A 345 LEU cc_start: 0.7851 (mm) cc_final: 0.7528 (pt) REVERT: A 405 MET cc_start: 0.8452 (ptp) cc_final: 0.8089 (ptp) REVERT: A 1154 LYS cc_start: 0.7636 (mmtp) cc_final: 0.7283 (pttp) REVERT: A 1192 GLN cc_start: 0.7720 (tt0) cc_final: 0.7294 (mt0) REVERT: A 1207 PHE cc_start: 0.7903 (m-10) cc_final: 0.7694 (m-10) REVERT: A 1263 ARG cc_start: 0.7364 (tpp-160) cc_final: 0.7078 (tpp-160) REVERT: A 1434 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8074 (tp) REVERT: A 1468 MET cc_start: 0.8268 (mtt) cc_final: 0.7855 (mtp) outliers start: 24 outliers final: 23 residues processed: 84 average time/residue: 0.0879 time to fit residues: 11.0233 Evaluate side-chains 86 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.123491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101069 restraints weight = 13305.653| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.17 r_work: 0.3165 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9293 Z= 0.132 Angle : 0.509 8.800 12636 Z= 0.252 Chirality : 0.039 0.227 1513 Planarity : 0.004 0.040 1541 Dihedral : 6.528 135.701 1265 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.48 % Allowed : 13.93 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.25), residues: 1145 helix: 2.49 (0.18), residues: 759 sheet: 0.92 (0.65), residues: 69 loop : 0.04 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1382 TYR 0.013 0.001 TYR A1126 PHE 0.013 0.001 PHE A1207 TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9293) covalent geometry : angle 0.50875 / 0.25 (12636) hydrogen bonds : bond 0.05084 / 3.49 ( 614) hydrogen bonds : angle 3.94730 / 2.95 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.351 Fit side-chains REVERT: A 231 MET cc_start: 0.7653 (mtp) cc_final: 0.7133 (mtp) REVERT: A 270 GLU cc_start: 0.8467 (tp30) cc_final: 0.7909 (mt-10) REVERT: A 345 LEU cc_start: 0.7841 (mm) cc_final: 0.7549 (pt) REVERT: A 405 MET cc_start: 0.8414 (ptp) cc_final: 0.8058 (ptp) REVERT: A 1154 LYS cc_start: 0.7606 (mmtp) cc_final: 0.7315 (pttp) REVERT: A 1192 GLN cc_start: 0.7605 (tt0) cc_final: 0.7176 (mt0) REVERT: A 1207 PHE cc_start: 0.7858 (m-10) cc_final: 0.7620 (m-10) REVERT: A 1434 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8050 (tp) REVERT: A 1468 MET cc_start: 0.8406 (mtt) cc_final: 0.7970 (mtp) outliers start: 24 outliers final: 22 residues processed: 86 average time/residue: 0.0796 time to fit residues: 10.4205 Evaluate side-chains 86 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 0.0060 chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 89 optimal weight: 0.0270 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104649 restraints weight = 13160.476| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.15 r_work: 0.3215 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9293 Z= 0.111 Angle : 0.489 8.446 12636 Z= 0.243 Chirality : 0.038 0.226 1513 Planarity : 0.004 0.040 1541 Dihedral : 6.384 131.143 1265 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.75 % Allowed : 14.65 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.25), residues: 1145 helix: 2.65 (0.18), residues: 759 sheet: 1.00 (0.67), residues: 64 loop : 0.16 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.014 0.001 TYR A1126 PHE 0.010 0.001 PHE A1207 TRP 0.011 0.001 TRP A 877 HIS 0.003 0.000 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9293) covalent geometry : angle 0.48905 / 0.24 (12636) hydrogen bonds : bond 0.04695 / 3.21 ( 614) hydrogen bonds : angle 3.80771 / 2.85 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.360 Fit side-chains REVERT: A 231 MET cc_start: 0.7556 (mtp) cc_final: 0.7139 (mtp) REVERT: A 270 GLU cc_start: 0.8470 (tp30) cc_final: 0.7922 (mt-10) REVERT: A 345 LEU cc_start: 0.7812 (mm) cc_final: 0.7550 (pt) REVERT: A 405 MET cc_start: 0.8342 (ptp) cc_final: 0.7997 (ptp) REVERT: A 690 ARG cc_start: 0.7730 (ptm160) cc_final: 0.7223 (ptm160) REVERT: A 833 ASP cc_start: 0.8280 (t0) cc_final: 0.8032 (t0) REVERT: A 1154 LYS cc_start: 0.7455 (mmtp) cc_final: 0.7196 (pttp) REVERT: A 1192 GLN cc_start: 0.7524 (tt0) cc_final: 0.7149 (mt0) REVERT: A 1207 PHE cc_start: 0.7764 (m-80) cc_final: 0.7543 (m-10) REVERT: A 1272 MET cc_start: 0.8163 (mmm) cc_final: 0.7742 (mmm) REVERT: A 1434 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7947 (tp) REVERT: A 1468 MET cc_start: 0.8491 (mtt) cc_final: 0.8004 (mtp) outliers start: 17 outliers final: 13 residues processed: 81 average time/residue: 0.0857 time to fit residues: 10.4467 Evaluate side-chains 79 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 90 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102918 restraints weight = 13160.525| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.16 r_work: 0.3187 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9293 Z= 0.131 Angle : 0.499 8.860 12636 Z= 0.247 Chirality : 0.039 0.214 1513 Planarity : 0.004 0.040 1541 Dihedral : 6.390 131.489 1265 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.25), residues: 1145 helix: 2.65 (0.18), residues: 759 sheet: 1.12 (0.65), residues: 69 loop : 0.16 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1382 TYR 0.018 0.001 TYR A1205 PHE 0.011 0.001 PHE A1207 TRP 0.010 0.001 TRP A 432 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9293) covalent geometry : angle 0.49938 / 0.25 (12636) hydrogen bonds : bond 0.04840 / 3.32 ( 614) hydrogen bonds : angle 3.85929 / 2.88 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1956.25 seconds wall clock time: 34 minutes 25.60 seconds (2065.60 seconds total)