Starting phenix.real_space_refine on Wed Feb 4 08:22:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vlu_32027/02_2026/7vlu_32027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vlu_32027/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vlu_32027/02_2026/7vlu_32027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vlu_32027/02_2026/7vlu_32027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vlu_32027/02_2026/7vlu_32027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vlu_32027/02_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-2.0-5952/lib/python3.9/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: 2.27, per 1000 atoms: 0.25 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: 0.89 Conformation dependent library (CDL) restraints added in 487.7 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: 0.22 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: 1.03 Time building geometry restraints manager: 1.14 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: 0.510 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.830 Find NCS groups from input model: 0.030 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.010 ------------------------------------------------------------------------------- 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= 0.196 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 : 3.97 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 covalent geometry : bond 0.00387 ( 9293) covalent geometry : angle 0.63454 (12636) hydrogen bonds : bond 0.12127 ( 614) hydrogen bonds : angle 6.24764 ( 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 : 0.272 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: 0.1087 time to fit residues: 23.0701 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 : 0.351 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3571 r_free = 0.3571 target = 0.122967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100493 restraints weight = 13195.898| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.13 r_work: 0.3158 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9293 Z= 0.190 Angle : 0.627 10.545 12636 Z= 0.312 Chirality : 0.043 0.262 1513 Planarity : 0.004 0.059 1541 Dihedral : 8.650 146.768 1366 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.27 % Allowed : 10.32 % Favored : 87.41 % 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: 1.05 (0.24), residues: 1145 helix: 1.39 (0.18), residues: 765 sheet: -0.57 (0.55), residues: 69 loop : -0.62 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1182 TYR 0.016 0.001 TYR A1126 PHE 0.015 0.001 PHE A1207 TRP 0.010 0.001 TRP A 230 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9293) covalent geometry : angle 0.62706 (12636) hydrogen bonds : bond 0.05903 ( 614) hydrogen bonds : angle 4.57252 ( 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 96 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.445 Fit side-chains REVERT: A 243 ILE cc_start: 0.8190 (mt) cc_final: 0.7892 (mp) REVERT: A 539 MET cc_start: 0.8003 (mmm) cc_final: 0.7354 (mmm) REVERT: A 764 GLU cc_start: 0.7783 (tp30) cc_final: 0.7193 (tp30) REVERT: A 1192 GLN cc_start: 0.7796 (tt0) cc_final: 0.7423 (mt0) REVERT: A 1272 MET cc_start: 0.8395 (mmt) cc_final: 0.8084 (mmm) REVERT: A 1398 SER cc_start: 0.8502 (m) cc_final: 0.8077 (p) REVERT: A 1468 MET cc_start: 0.8342 (mtt) cc_final: 0.7948 (mtp) outliers start: 22 outliers final: 11 residues processed: 94 average time/residue: 0.0877 time to fit residues: 12.2042 Evaluate side-chains 75 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 0.7980 chunk 39 optimal weight: 0.0670 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 46 optimal weight: 0.0370 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 GLN A1256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104436 restraints weight = 12983.098| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.12 r_work: 0.3214 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9293 Z= 0.127 Angle : 0.528 8.313 12636 Z= 0.264 Chirality : 0.039 0.210 1513 Planarity : 0.004 0.056 1541 Dihedral : 8.045 139.867 1358 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.37 % Allowed : 10.94 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.24), residues: 1145 helix: 2.18 (0.18), residues: 759 sheet: -0.28 (0.56), residues: 69 loop : -0.42 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1382 TYR 0.009 0.001 TYR A1205 PHE 0.016 0.001 PHE A1445 TRP 0.005 0.001 TRP A 980 HIS 0.003 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9293) covalent geometry : angle 0.52830 (12636) hydrogen bonds : bond 0.05202 ( 614) hydrogen bonds : angle 4.14555 ( 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 102 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.368 Fit side-chains REVERT: A 230 TRP cc_start: 0.5902 (OUTLIER) cc_final: 0.5541 (p-90) REVERT: A 243 ILE cc_start: 0.8332 (mt) cc_final: 0.8099 (mt) REVERT: A 323 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7160 (tt0) REVERT: A 405 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8144 (ptp) REVERT: A 764 GLU cc_start: 0.7756 (tp30) cc_final: 0.7239 (tp30) REVERT: A 833 ASP cc_start: 0.8274 (t0) cc_final: 0.7048 (t70) REVERT: A 1108 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 1192 GLN cc_start: 0.7619 (tt0) cc_final: 0.7355 (mt0) REVERT: A 1254 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7547 (tt) REVERT: A 1272 MET cc_start: 0.8243 (mmt) cc_final: 0.7915 (mmm) REVERT: A 1398 SER cc_start: 0.8547 (m) cc_final: 0.8021 (p) REVERT: A 1434 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8153 (tp) REVERT: A 1444 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 1468 MET cc_start: 0.8364 (mtt) cc_final: 0.7917 (mtp) outliers start: 23 outliers final: 7 residues processed: 95 average time/residue: 0.0805 time to fit residues: 11.6193 Evaluate side-chains 81 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 1254 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1444 ASN 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: 3.9990 chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.119765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097065 restraints weight = 13415.301| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.15 r_work: 0.3100 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9293 Z= 0.237 Angle : 0.628 11.026 12636 Z= 0.313 Chirality : 0.044 0.206 1513 Planarity : 0.004 0.053 1541 Dihedral : 8.092 146.918 1356 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.99 % Allowed : 11.87 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1145 helix: 1.99 (0.18), residues: 759 sheet: 0.07 (0.59), residues: 69 loop : -0.38 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1382 TYR 0.014 0.001 TYR A1205 PHE 0.015 0.002 PHE A1207 TRP 0.009 0.001 TRP A 979 HIS 0.007 0.001 HIS A1001 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 9293) covalent geometry : angle 0.62822 (12636) hydrogen bonds : bond 0.06031 ( 614) hydrogen bonds : angle 4.38722 ( 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 94 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.365 Fit side-chains REVERT: A 230 TRP cc_start: 0.5788 (OUTLIER) cc_final: 0.5408 (p-90) REVERT: A 243 ILE cc_start: 0.8433 (mt) cc_final: 0.8155 (mp) REVERT: A 539 MET cc_start: 0.7610 (mmm) cc_final: 0.7299 (mmt) REVERT: A 1192 GLN cc_start: 0.7781 (tt0) cc_final: 0.7345 (mt0) REVERT: A 1263 ARG cc_start: 0.7436 (tpp-160) cc_final: 0.7133 (tpp-160) REVERT: A 1272 MET cc_start: 0.8427 (mmt) cc_final: 0.8128 (mmm) REVERT: A 1398 SER cc_start: 0.8788 (m) cc_final: 0.8321 (p) REVERT: A 1434 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8278 (tp) REVERT: A 1468 MET cc_start: 0.8298 (mtt) cc_final: 0.8024 (mtp) outliers start: 29 outliers final: 17 residues processed: 92 average time/residue: 0.0707 time to fit residues: 10.2581 Evaluate side-chains 78 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP 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 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 1219 THR Chi-restraints excluded: chain A residue 1244 VAL 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: 3.9990 chunk 85 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099160 restraints weight = 13206.160| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.21 r_work: 0.3126 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3087 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= 0.159 Angle : 0.538 9.370 12636 Z= 0.269 Chirality : 0.040 0.211 1513 Planarity : 0.004 0.049 1541 Dihedral : 7.898 144.515 1356 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.48 % Allowed : 12.80 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.25), residues: 1145 helix: 2.23 (0.18), residues: 759 sheet: 0.31 (0.61), residues: 69 loop : -0.33 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1382 TYR 0.011 0.001 TYR A1205 PHE 0.013 0.001 PHE A1207 TRP 0.008 0.001 TRP A 877 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9293) covalent geometry : angle 0.53839 (12636) hydrogen bonds : bond 0.05493 ( 614) hydrogen bonds : angle 4.15994 ( 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 89 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.369 Fit side-chains REVERT: A 230 TRP cc_start: 0.5825 (OUTLIER) cc_final: 0.5445 (p-90) REVERT: A 243 ILE cc_start: 0.8458 (mt) cc_final: 0.8251 (mt) REVERT: A 539 MET cc_start: 0.7608 (mmm) cc_final: 0.7380 (mmt) REVERT: A 1192 GLN cc_start: 0.7707 (tt0) cc_final: 0.7268 (mt0) REVERT: A 1272 MET cc_start: 0.8273 (mmt) cc_final: 0.7954 (mmm) REVERT: A 1398 SER cc_start: 0.8744 (m) cc_final: 0.8166 (p) REVERT: A 1434 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8240 (tp) REVERT: A 1468 MET cc_start: 0.8231 (mtt) cc_final: 0.7935 (mtp) outliers start: 24 outliers final: 16 residues processed: 87 average time/residue: 0.0753 time to fit residues: 10.1404 Evaluate side-chains 78 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP 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 561 ASN 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 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1244 VAL 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 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099845 restraints weight = 13377.392| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.15 r_work: 0.3154 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3200 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 : 0.516 9.072 12636 Z= 0.258 Chirality : 0.039 0.207 1513 Planarity : 0.004 0.046 1541 Dihedral : 7.727 144.119 1354 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.06 % Allowed : 13.62 % 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: 2.32 (0.25), residues: 1145 helix: 2.34 (0.19), residues: 759 sheet: 0.55 (0.63), residues: 69 loop : -0.21 (0.35), 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 0.011 0.001 PHE A1207 TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9293) covalent geometry : angle 0.51616 (12636) hydrogen bonds : bond 0.05296 ( 614) hydrogen bonds : angle 4.06919 ( 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 85 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.451 Fit side-chains REVERT: A 230 TRP cc_start: 0.5945 (OUTLIER) cc_final: 0.5510 (p-90) REVERT: A 243 ILE cc_start: 0.8479 (mt) cc_final: 0.8269 (mt) REVERT: A 270 GLU cc_start: 0.8539 (tp30) cc_final: 0.7929 (mt-10) REVERT: A 323 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7142 (tt0) REVERT: A 1192 GLN cc_start: 0.7599 (tt0) cc_final: 0.7159 (mt0) REVERT: A 1272 MET cc_start: 0.8266 (mmt) cc_final: 0.7927 (mmm) REVERT: A 1398 SER cc_start: 0.8745 (m) cc_final: 0.8153 (p) REVERT: A 1434 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8203 (tp) REVERT: A 1468 MET cc_start: 0.8212 (mtt) cc_final: 0.7815 (mtp) outliers start: 20 outliers final: 15 residues processed: 82 average time/residue: 0.0800 time to fit residues: 9.9229 Evaluate side-chains 77 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 106 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099905 restraints weight = 13337.654| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.16 r_work: 0.3152 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3190 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 : 0.516 9.072 12636 Z= 0.258 Chirality : 0.039 0.207 1513 Planarity : 0.004 0.046 1541 Dihedral : 7.732 144.119 1354 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.75 % Allowed : 13.62 % Favored : 84.62 % 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: 2.32 (0.25), residues: 1145 helix: 2.34 (0.19), residues: 759 sheet: 0.55 (0.63), residues: 69 loop : -0.21 (0.35), 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 0.011 0.001 PHE A1207 TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9293) covalent geometry : angle 0.51609 (12636) hydrogen bonds : bond 0.05296 ( 614) hydrogen bonds : angle 4.06917 ( 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 77 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.353 Fit side-chains REVERT: A 230 TRP cc_start: 0.5959 (OUTLIER) cc_final: 0.5521 (p-90) REVERT: A 243 ILE cc_start: 0.8486 (mt) cc_final: 0.8276 (mt) REVERT: A 270 GLU cc_start: 0.8538 (tp30) cc_final: 0.7930 (mt-10) REVERT: A 323 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7147 (tt0) REVERT: A 1192 GLN cc_start: 0.7598 (tt0) cc_final: 0.7159 (mt0) REVERT: A 1272 MET cc_start: 0.8264 (mmt) cc_final: 0.7927 (mmm) REVERT: A 1398 SER cc_start: 0.8747 (m) cc_final: 0.8156 (p) REVERT: A 1434 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8199 (tp) REVERT: A 1468 MET cc_start: 0.8209 (mtt) cc_final: 0.7810 (mtp) outliers start: 17 outliers final: 15 residues processed: 74 average time/residue: 0.0673 time to fit residues: 7.6531 Evaluate side-chains 77 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 82 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 105 optimal weight: 0.0470 chunk 48 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099629 restraints weight = 13078.110| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.23 r_work: 0.3142 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3196 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= 0.137 Angle : 0.515 9.069 12636 Z= 0.258 Chirality : 0.039 0.207 1513 Planarity : 0.004 0.045 1541 Dihedral : 7.753 144.119 1354 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.86 % Allowed : 13.62 % 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: 2.33 (0.25), residues: 1145 helix: 2.35 (0.19), residues: 759 sheet: 0.55 (0.63), residues: 69 loop : -0.20 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1382 TYR 0.009 0.001 TYR A1126 PHE 0.010 0.001 PHE A1207 TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9293) covalent geometry : angle 0.51540 (12636) hydrogen bonds : bond 0.05291 ( 614) hydrogen bonds : angle 4.06938 ( 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 78 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.368 Fit side-chains REVERT: A 230 TRP cc_start: 0.5949 (OUTLIER) cc_final: 0.5504 (p-90) REVERT: A 243 ILE cc_start: 0.8487 (mt) cc_final: 0.8277 (mt) REVERT: A 323 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7141 (tt0) REVERT: A 1192 GLN cc_start: 0.7591 (tt0) cc_final: 0.7154 (mt0) REVERT: A 1272 MET cc_start: 0.8263 (mmt) cc_final: 0.7924 (mmm) REVERT: A 1398 SER cc_start: 0.8742 (m) cc_final: 0.8154 (p) REVERT: A 1434 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8198 (tp) REVERT: A 1468 MET cc_start: 0.8191 (mtt) cc_final: 0.7798 (mtp) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.0753 time to fit residues: 8.7859 Evaluate side-chains 76 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 0.0170 chunk 106 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098052 restraints weight = 13382.731| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.15 r_work: 0.3125 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3282 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= 0.185 Angle : 0.554 10.103 12636 Z= 0.277 Chirality : 0.041 0.199 1513 Planarity : 0.004 0.044 1541 Dihedral : 7.739 146.806 1354 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.86 % Allowed : 13.93 % Favored : 84.21 % 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: 2.21 (0.25), residues: 1145 helix: 2.23 (0.18), residues: 759 sheet: 0.65 (0.64), residues: 69 loop : -0.19 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1382 TYR 0.020 0.001 TYR A1205 PHE 0.014 0.001 PHE A1207 TRP 0.008 0.001 TRP A 980 HIS 0.005 0.001 HIS A1001 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9293) covalent geometry : angle 0.55379 (12636) hydrogen bonds : bond 0.05554 ( 614) hydrogen bonds : angle 4.16922 ( 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 81 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.328 Fit side-chains REVERT: A 243 ILE cc_start: 0.8477 (mt) cc_final: 0.8270 (mt) REVERT: A 1192 GLN cc_start: 0.7736 (tt0) cc_final: 0.7302 (mt0) REVERT: A 1398 SER cc_start: 0.8809 (m) cc_final: 0.8214 (p) REVERT: A 1434 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8225 (tp) REVERT: A 1455 LEU cc_start: 0.7548 (mp) cc_final: 0.7324 (mp) REVERT: A 1468 MET cc_start: 0.8251 (mtt) cc_final: 0.7951 (mtp) outliers start: 18 outliers final: 17 residues processed: 79 average time/residue: 0.0741 time to fit residues: 9.0437 Evaluate side-chains 79 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 0.4980 chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101138 restraints weight = 13051.416| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.24 r_work: 0.3165 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3429 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= 0.123 Angle : 0.504 9.025 12636 Z= 0.253 Chirality : 0.038 0.206 1513 Planarity : 0.004 0.044 1541 Dihedral : 7.545 143.665 1354 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.24 % Allowed : 15.07 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.25), residues: 1145 helix: 2.47 (0.19), residues: 759 sheet: 0.81 (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 0.015 0.001 TYR A1126 PHE 0.011 0.001 PHE A1207 TRP 0.008 0.001 TRP A 877 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9293) covalent geometry : angle 0.50372 (12636) hydrogen bonds : bond 0.05084 ( 614) hydrogen bonds : angle 3.98681 ( 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 78 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.367 Fit side-chains REVERT: A 243 ILE cc_start: 0.8456 (mt) cc_final: 0.8247 (mt) REVERT: A 690 ARG cc_start: 0.7682 (ptm160) cc_final: 0.7164 (ptm160) REVERT: A 1192 GLN cc_start: 0.7595 (tt0) cc_final: 0.7193 (mt0) REVERT: A 1207 PHE cc_start: 0.7875 (m-80) cc_final: 0.7650 (m-10) REVERT: A 1398 SER cc_start: 0.8726 (m) cc_final: 0.8116 (p) REVERT: A 1434 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 1468 MET cc_start: 0.8413 (mtt) cc_final: 0.7974 (mtp) outliers start: 12 outliers final: 10 residues processed: 77 average time/residue: 0.0878 time to fit residues: 10.3105 Evaluate side-chains 75 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 829 VAL 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 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: 1.9990 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102147 restraints weight = 13087.381| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.14 r_work: 0.3182 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9293 Z= 0.124 Angle : 0.499 8.478 12636 Z= 0.250 Chirality : 0.038 0.194 1513 Planarity : 0.004 0.043 1541 Dihedral : 7.433 141.836 1354 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.24 % Allowed : 15.07 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.25), residues: 1145 helix: 2.54 (0.18), residues: 759 sheet: 0.90 (0.64), residues: 69 loop : -0.01 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.014 0.001 TYR A1205 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 covalent geometry : bond 0.00266 ( 9293) covalent geometry : angle 0.49874 (12636) hydrogen bonds : bond 0.04955 ( 614) hydrogen bonds : angle 3.94520 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.39 seconds wall clock time: 34 minutes 27.70 seconds (2067.70 seconds total)