Starting phenix.real_space_refine on Fri Mar 14 07:23:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vlu_32027/03_2025/7vlu_32027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vlu_32027/03_2025/7vlu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vlu_32027/03_2025/7vlu_32027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vlu_32027/03_2025/7vlu_32027.map" model { file = "/net/cci-nas-00/data/ceres_data/7vlu_32027/03_2025/7vlu_32027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vlu_32027/03_2025/7vlu_32027.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 4} 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: 5.27, per 1000 atoms: 0.58 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.19 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: 3.40 Time building geometry restraints manager: 2.55 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: 5394 28.13 - 56.25: 167 56.25 - 84.38: 13 84.38 - 112.50: 1 112.50 - 140.62: 1 Dihedral angle restraints: 5576 sinusoidal: 2208 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 5573 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: 0.400 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.600 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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= 0.238 Angle : 0.635 14.936 12636 Z= 0.316 Chirality : 0.041 0.285 1513 Planarity : 0.004 0.054 1541 Dihedral : 13.044 140.625 3394 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (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 TRP 0.008 0.001 TRP A 230 HIS 0.006 0.001 HIS A1001 PHE 0.010 0.001 PHE A 424 TYR 0.008 0.001 TYR A1257 ARG 0.002 0.000 ARG A 820 *********************** 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 : 0.987 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: 0.2486 time to fit residues: 53.0939 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 : 0.995 ------------------------------------------------------------------------------- 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 97 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098880 restraints weight = 13129.898| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.11 r_work: 0.3125 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9293 Z= 0.344 Angle : 0.653 11.905 12636 Z= 0.325 Chirality : 0.045 0.301 1513 Planarity : 0.005 0.060 1541 Dihedral : 8.761 147.537 1366 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.58 % Allowed : 10.11 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1145 helix: 1.20 (0.18), residues: 765 sheet: -0.63 (0.55), residues: 69 loop : -0.69 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 230 HIS 0.006 0.001 HIS A1065 PHE 0.014 0.002 PHE A1207 TYR 0.014 0.001 TYR A1126 ARG 0.004 0.001 ARG A1182 *********************** 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 97 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 1.011 Fit side-chains REVERT: A 230 TRP cc_start: 0.6152 (OUTLIER) cc_final: 0.5497 (p-90) REVERT: A 243 ILE cc_start: 0.8185 (mt) cc_final: 0.7889 (mp) REVERT: A 539 MET cc_start: 0.7980 (mmm) cc_final: 0.7314 (mmm) REVERT: A 764 GLU cc_start: 0.7800 (tp30) cc_final: 0.7184 (tp30) REVERT: A 1192 GLN cc_start: 0.7806 (tt0) cc_final: 0.7409 (mt0) REVERT: A 1252 LEU cc_start: 0.7981 (mt) cc_final: 0.7776 (mp) REVERT: A 1272 MET cc_start: 0.8436 (mmt) cc_final: 0.8123 (mmm) REVERT: A 1398 SER cc_start: 0.8493 (m) cc_final: 0.8076 (p) REVERT: A 1468 MET cc_start: 0.8308 (mtt) cc_final: 0.7928 (mtp) outliers start: 25 outliers final: 10 residues processed: 95 average time/residue: 0.2016 time to fit residues: 28.2178 Evaluate side-chains 73 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3578 r_free = 0.3578 target = 0.123210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099887 restraints weight = 13015.801| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.23 r_work: 0.3144 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9293 Z= 0.232 Angle : 0.560 8.391 12636 Z= 0.280 Chirality : 0.041 0.208 1513 Planarity : 0.004 0.058 1541 Dihedral : 8.210 142.720 1360 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.58 % Allowed : 11.15 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1145 helix: 1.99 (0.18), residues: 759 sheet: -0.26 (0.56), residues: 69 loop : -0.46 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 230 HIS 0.004 0.001 HIS A1065 PHE 0.013 0.001 PHE A1207 TYR 0.011 0.001 TYR A1126 ARG 0.009 0.000 ARG A1382 *********************** 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 100 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.049 Fit side-chains REVERT: A 243 ILE cc_start: 0.8350 (mt) cc_final: 0.8116 (mt) REVERT: A 323 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7151 (tt0) REVERT: A 405 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8306 (ptp) REVERT: A 539 MET cc_start: 0.7522 (mmm) cc_final: 0.6953 (mmm) REVERT: A 1192 GLN cc_start: 0.7716 (tt0) cc_final: 0.7346 (mt0) REVERT: A 1252 LEU cc_start: 0.7850 (mt) cc_final: 0.7644 (mp) REVERT: A 1254 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7477 (tt) REVERT: A 1272 MET cc_start: 0.8298 (mmt) cc_final: 0.7941 (mmm) REVERT: A 1398 SER cc_start: 0.8634 (m) cc_final: 0.8205 (p) REVERT: A 1434 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8210 (tp) REVERT: A 1468 MET cc_start: 0.8197 (mtt) cc_final: 0.7830 (mtp) outliers start: 25 outliers final: 13 residues processed: 93 average time/residue: 0.1819 time to fit residues: 25.8419 Evaluate side-chains 81 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 MET 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097324 restraints weight = 13291.411| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.13 r_work: 0.3120 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9293 Z= 0.318 Angle : 0.598 9.882 12636 Z= 0.297 Chirality : 0.042 0.203 1513 Planarity : 0.004 0.053 1541 Dihedral : 8.088 146.499 1357 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.58 % Allowed : 11.87 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.25), residues: 1145 helix: 2.00 (0.18), residues: 759 sheet: 0.24 (0.61), residues: 69 loop : -0.40 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 979 HIS 0.006 0.001 HIS A1001 PHE 0.014 0.001 PHE A1207 TYR 0.013 0.001 TYR A1205 ARG 0.007 0.000 ARG A1382 *********************** 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: 25 poor density : 67 time to evaluate : 1.055 Fit side-chains REVERT: A 243 ILE cc_start: 0.8527 (mt) cc_final: 0.8316 (mt) REVERT: A 1192 GLN cc_start: 0.7868 (tt0) cc_final: 0.7397 (mt0) REVERT: A 1272 MET cc_start: 0.8464 (mmt) cc_final: 0.8121 (mmm) REVERT: A 1282 LEU cc_start: 0.8487 (mp) cc_final: 0.8283 (mt) REVERT: A 1398 SER cc_start: 0.8885 (m) cc_final: 0.8430 (p) REVERT: A 1434 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8314 (tp) REVERT: A 1468 MET cc_start: 0.8405 (mtt) cc_final: 0.8030 (mtp) outliers start: 25 outliers final: 18 residues processed: 90 average time/residue: 0.1712 time to fit residues: 23.9112 Evaluate side-chains 80 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 580 THR 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 989 LEU Chi-restraints excluded: chain A residue 1115 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3573 r_free = 0.3573 target = 0.123007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100515 restraints weight = 13187.024| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.14 r_work: 0.3162 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9293 Z= 0.192 Angle : 0.521 9.487 12636 Z= 0.259 Chirality : 0.039 0.208 1513 Planarity : 0.004 0.047 1541 Dihedral : 7.818 143.298 1357 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.27 % Allowed : 12.90 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.25), residues: 1145 helix: 2.31 (0.18), residues: 759 sheet: 0.48 (0.62), residues: 69 loop : -0.26 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1065 PHE 0.010 0.001 PHE A1207 TYR 0.007 0.001 TYR A1205 ARG 0.007 0.000 ARG A1382 *********************** 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 92 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 1.107 Fit side-chains REVERT: A 243 ILE cc_start: 0.8501 (mt) cc_final: 0.8285 (mt) REVERT: A 270 GLU cc_start: 0.8504 (tp30) cc_final: 0.7910 (mt-10) REVERT: A 405 MET cc_start: 0.8595 (ptp) cc_final: 0.8191 (ptp) REVERT: A 690 ARG cc_start: 0.7780 (ptm160) cc_final: 0.7103 (ptm160) REVERT: A 1192 GLN cc_start: 0.7659 (tt0) cc_final: 0.7222 (mt0) REVERT: A 1207 PHE cc_start: 0.8023 (m-10) cc_final: 0.7748 (m-10) REVERT: A 1398 SER cc_start: 0.8776 (m) cc_final: 0.8201 (p) REVERT: A 1434 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8219 (tp) REVERT: A 1468 MET cc_start: 0.8485 (mtt) cc_final: 0.8008 (mtp) outliers start: 22 outliers final: 13 residues processed: 89 average time/residue: 0.1829 time to fit residues: 24.8337 Evaluate side-chains 74 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 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 829 VAL Chi-restraints excluded: chain A residue 843 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.0570 chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100367 restraints weight = 13201.795| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.14 r_work: 0.3165 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9293 Z= 0.196 Angle : 0.518 9.171 12636 Z= 0.256 Chirality : 0.039 0.197 1513 Planarity : 0.004 0.043 1541 Dihedral : 7.644 143.363 1355 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.96 % Allowed : 14.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.25), residues: 1145 helix: 2.38 (0.19), residues: 759 sheet: 0.70 (0.64), residues: 69 loop : -0.18 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1001 PHE 0.011 0.001 PHE A1207 TYR 0.012 0.001 TYR A1126 ARG 0.006 0.000 ARG A1382 *********************** 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 83 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.975 Fit side-chains REVERT: A 243 ILE cc_start: 0.8505 (mt) cc_final: 0.8297 (mt) REVERT: A 405 MET cc_start: 0.8502 (ptp) cc_final: 0.8114 (ptp) REVERT: A 1192 GLN cc_start: 0.7656 (tt0) cc_final: 0.7233 (mt0) REVERT: A 1207 PHE cc_start: 0.8045 (m-10) cc_final: 0.7685 (m-10) REVERT: A 1398 SER cc_start: 0.8804 (m) cc_final: 0.8221 (p) REVERT: A 1434 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8240 (tp) REVERT: A 1468 MET cc_start: 0.8476 (mtt) cc_final: 0.8007 (mtp) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.1977 time to fit residues: 24.0507 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 : 1.106 ------------------------------------------------------------------------------- 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 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 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 1115 LEU Chi-restraints excluded: chain A residue 1256 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100744 restraints weight = 13270.128| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.17 r_work: 0.3171 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3443 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= 0.193 Angle : 0.512 9.011 12636 Z= 0.254 Chirality : 0.039 0.199 1513 Planarity : 0.004 0.043 1541 Dihedral : 7.508 142.061 1354 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.48 % Allowed : 14.24 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.25), residues: 1145 helix: 2.43 (0.18), residues: 759 sheet: 0.84 (0.65), residues: 69 loop : -0.05 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1065 PHE 0.010 0.001 PHE A1207 TYR 0.014 0.001 TYR A1126 ARG 0.005 0.000 ARG A1382 *********************** 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 86 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.986 Fit side-chains REVERT: A 231 MET cc_start: 0.7278 (mmm) cc_final: 0.6996 (mmm) REVERT: A 243 ILE cc_start: 0.8521 (mt) cc_final: 0.8313 (mt) REVERT: A 270 GLU cc_start: 0.8498 (tp30) cc_final: 0.7939 (mt-10) REVERT: A 405 MET cc_start: 0.8465 (ptp) cc_final: 0.8126 (ptp) REVERT: A 690 ARG cc_start: 0.7805 (ptm160) cc_final: 0.7329 (ptm160) REVERT: A 1192 GLN cc_start: 0.7627 (tt0) cc_final: 0.7203 (mt0) REVERT: A 1207 PHE cc_start: 0.7922 (m-10) cc_final: 0.7583 (m-10) REVERT: A 1272 MET cc_start: 0.8140 (mmm) cc_final: 0.7843 (mmm) REVERT: A 1398 SER cc_start: 0.8822 (m) cc_final: 0.8225 (p) REVERT: A 1434 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8113 (tp) REVERT: A 1468 MET cc_start: 0.8478 (mtt) cc_final: 0.7985 (mtp) REVERT: A 1483 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7616 (tp) outliers start: 24 outliers final: 17 residues processed: 84 average time/residue: 0.1813 time to fit residues: 23.0282 Evaluate side-chains 80 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 319 SER 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 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 989 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1256 ASN 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 1483 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 14 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099283 restraints weight = 13462.907| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.16 r_work: 0.3150 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9293 Z= 0.237 Angle : 0.529 9.198 12636 Z= 0.262 Chirality : 0.040 0.191 1513 Planarity : 0.004 0.042 1541 Dihedral : 7.484 141.952 1354 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.48 % Allowed : 15.07 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.25), residues: 1145 helix: 2.41 (0.18), residues: 759 sheet: 0.87 (0.64), residues: 69 loop : -0.02 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 877 HIS 0.005 0.001 HIS A1065 PHE 0.012 0.001 PHE A1207 TYR 0.010 0.001 TYR A1126 ARG 0.004 0.000 ARG A1382 *********************** 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 87 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 1.078 Fit side-chains REVERT: A 243 ILE cc_start: 0.8513 (mt) cc_final: 0.8309 (mt) REVERT: A 270 GLU cc_start: 0.8484 (tp30) cc_final: 0.7912 (mt-10) REVERT: A 345 LEU cc_start: 0.7731 (mm) cc_final: 0.7405 (pt) REVERT: A 405 MET cc_start: 0.8451 (ptp) cc_final: 0.8072 (ptp) REVERT: A 1192 GLN cc_start: 0.7631 (tt0) cc_final: 0.7231 (mt0) REVERT: A 1207 PHE cc_start: 0.7904 (m-80) cc_final: 0.7644 (m-10) REVERT: A 1398 SER cc_start: 0.8809 (m) cc_final: 0.8207 (p) REVERT: A 1434 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8117 (tp) REVERT: A 1468 MET cc_start: 0.8480 (mtt) cc_final: 0.8026 (mtp) REVERT: A 1483 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7593 (tp) outliers start: 24 outliers final: 20 residues processed: 85 average time/residue: 0.1846 time to fit residues: 23.7395 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 : 1.069 ------------------------------------------------------------------------------- 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 319 SER 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 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 1097 ASN Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1256 ASN 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 1483 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 84 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098991 restraints weight = 13307.963| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.15 r_work: 0.3144 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9293 Z= 0.254 Angle : 0.546 10.503 12636 Z= 0.269 Chirality : 0.040 0.195 1513 Planarity : 0.004 0.042 1541 Dihedral : 7.447 141.493 1354 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.48 % Allowed : 15.07 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.25), residues: 1145 helix: 2.38 (0.18), residues: 759 sheet: 0.86 (0.64), residues: 69 loop : -0.01 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 980 HIS 0.005 0.001 HIS A1065 PHE 0.011 0.001 PHE A1207 TYR 0.014 0.001 TYR A1126 ARG 0.004 0.000 ARG A1382 *********************** 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 86 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.988 Fit side-chains REVERT: A 243 ILE cc_start: 0.8547 (mt) cc_final: 0.8336 (mt) REVERT: A 270 GLU cc_start: 0.8507 (tp30) cc_final: 0.7936 (mt-10) REVERT: A 345 LEU cc_start: 0.7842 (mm) cc_final: 0.7513 (pt) REVERT: A 405 MET cc_start: 0.8463 (ptp) cc_final: 0.8087 (ptp) REVERT: A 1192 GLN cc_start: 0.7710 (tt0) cc_final: 0.7286 (mt0) REVERT: A 1207 PHE cc_start: 0.7911 (m-80) cc_final: 0.7610 (m-10) REVERT: A 1272 MET cc_start: 0.7981 (mmm) cc_final: 0.7741 (mmm) REVERT: A 1398 SER cc_start: 0.8906 (m) cc_final: 0.8330 (p) REVERT: A 1434 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8138 (tp) REVERT: A 1468 MET cc_start: 0.8314 (mtt) cc_final: 0.7900 (mtp) REVERT: A 1483 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7619 (tp) outliers start: 24 outliers final: 19 residues processed: 84 average time/residue: 0.1803 time to fit residues: 22.8358 Evaluate side-chains 82 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 319 SER 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 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 1097 ASN Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1256 ASN 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 1483 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 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.0000 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 GLN A 867 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103382 restraints weight = 13286.989| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.16 r_work: 0.3202 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9293 Z= 0.150 Angle : 0.505 9.893 12636 Z= 0.248 Chirality : 0.038 0.203 1513 Planarity : 0.004 0.041 1541 Dihedral : 7.212 135.392 1354 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.34 % Allowed : 16.51 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.25), residues: 1145 helix: 2.60 (0.18), residues: 759 sheet: 1.05 (0.67), residues: 64 loop : 0.12 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 230 HIS 0.003 0.000 HIS A1001 PHE 0.010 0.001 PHE A1207 TYR 0.014 0.001 TYR A1126 ARG 0.006 0.000 ARG A1382 ********************** 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 81 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.980 Fit side-chains REVERT: A 243 ILE cc_start: 0.8457 (mt) cc_final: 0.8248 (mt) REVERT: A 270 GLU cc_start: 0.8475 (tp30) cc_final: 0.7925 (mt-10) REVERT: A 345 LEU cc_start: 0.7810 (mm) cc_final: 0.7474 (pt) REVERT: A 405 MET cc_start: 0.8348 (ptp) cc_final: 0.8005 (ptp) REVERT: A 690 ARG cc_start: 0.7722 (ptm160) cc_final: 0.7221 (ptm160) REVERT: A 833 ASP cc_start: 0.8396 (t0) cc_final: 0.7757 (t0) REVERT: A 1192 GLN cc_start: 0.7537 (tt0) cc_final: 0.7171 (mt0) REVERT: A 1207 PHE cc_start: 0.7921 (m-80) cc_final: 0.7668 (m-10) REVERT: A 1272 MET cc_start: 0.7865 (mmm) cc_final: 0.7639 (mmm) REVERT: A 1398 SER cc_start: 0.8805 (m) cc_final: 0.8183 (p) REVERT: A 1468 MET cc_start: 0.8717 (mtt) cc_final: 0.8331 (mtp) outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 0.1861 time to fit residues: 22.3062 Evaluate side-chains 76 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 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 993 MET Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 HIS ** A1271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.101588 restraints weight = 13238.709| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.14 r_work: 0.3176 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3729 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= 0.201 Angle : 0.521 9.699 12636 Z= 0.256 Chirality : 0.039 0.182 1513 Planarity : 0.004 0.042 1541 Dihedral : 7.206 134.768 1354 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.34 % Allowed : 17.03 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.25), residues: 1145 helix: 2.58 (0.18), residues: 759 sheet: 1.22 (0.65), residues: 69 loop : 0.14 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 980 HIS 0.004 0.001 HIS A1065 PHE 0.012 0.001 PHE A1207 TYR 0.014 0.001 TYR A1205 ARG 0.005 0.000 ARG A1382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4100.98 seconds wall clock time: 71 minutes 16.45 seconds (4276.45 seconds total)