Starting phenix.real_space_refine on Fri Dec 8 20:51:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/12_2023/7vlu_32027.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/12_2023/7vlu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/12_2023/7vlu_32027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/12_2023/7vlu_32027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/12_2023/7vlu_32027.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/12_2023/7vlu_32027.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9110 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9110 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'ESV': 1, 'Y01': 1} Classifications: {'peptide': 1159, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 34, 'TRANS': 1124, None: 6} Not linked: pdbres="THR A1543 " pdbres="Y01 A1601 " Not linked: pdbres="Y01 A1601 " pdbres="ADP A1602 " Not linked: pdbres="ADP A1602 " pdbres=" MG A1603 " Not linked: pdbres=" MG A1603 " pdbres=" MG A1604 " Not linked: pdbres=" MG A1604 " pdbres="ATP A1605 " Not linked: pdbres="ATP A1605 " pdbres="ESV A1606 " 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 Time building chain proxies: 5.50, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 3.83 Conformation dependent library (CDL) restraints added in 1.6 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: 0.92 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: 2.91 Time building geometry restraints manager: 4.11 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: 100.52 - 115.72: 6179 115.72 - 130.92: 6408 130.92 - 146.12: 48 146.12 - 161.32: 0 161.32 - 176.52: 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 2.440 ... (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: 0.580 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: 2.280 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.410 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.340 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.064 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 158 average time/residue: 0.2469 time to fit residues: 52.4882 Evaluate side-chains 72 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1084 time to fit residues: 2.6279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.0980 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 824 GLN A1444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9293 Z= 0.327 Angle : 0.648 11.029 12636 Z= 0.323 Chirality : 0.044 0.246 1513 Planarity : 0.005 0.061 1541 Dihedral : 8.281 143.939 1352 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.17 % Allowed : 10.84 % Favored : 87.00 % 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: 1.00 (0.24), residues: 1145 helix: 1.34 (0.18), residues: 765 sheet: -0.47 (0.56), residues: 69 loop : -0.65 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1260 HIS 0.006 0.001 HIS A1379 PHE 0.015 0.002 PHE A1207 TYR 0.015 0.001 TYR A1126 ARG 0.004 0.001 ARG A 304 *********************** 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 94 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 1.101 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 93 average time/residue: 0.2086 time to fit residues: 28.3412 Evaluate side-chains 70 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0859 time to fit residues: 2.5848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9293 Z= 0.230 Angle : 0.562 9.474 12636 Z= 0.280 Chirality : 0.041 0.213 1513 Planarity : 0.004 0.059 1541 Dihedral : 8.057 140.173 1352 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.65 % Allowed : 11.87 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.24), residues: 1145 helix: 2.01 (0.18), residues: 759 sheet: -0.19 (0.57), residues: 69 loop : -0.42 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 980 HIS 0.005 0.001 HIS A1379 PHE 0.012 0.001 PHE A1207 TYR 0.011 0.001 TYR A1205 ARG 0.002 0.000 ARG A 860 *********************** 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 84 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.992 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 79 average time/residue: 0.1891 time to fit residues: 22.4164 Evaluate side-chains 65 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0835 time to fit residues: 1.9036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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** A1256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2840 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= 0.277 Angle : 0.559 9.668 12636 Z= 0.280 Chirality : 0.041 0.205 1513 Planarity : 0.004 0.054 1541 Dihedral : 7.921 139.431 1352 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.44 % Allowed : 13.11 % Favored : 85.45 % 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: 1.95 (0.25), residues: 1145 helix: 2.07 (0.18), residues: 759 sheet: 0.23 (0.60), residues: 69 loop : -0.32 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 727 HIS 0.005 0.001 HIS A1001 PHE 0.014 0.001 PHE A1207 TYR 0.012 0.001 TYR A1205 ARG 0.003 0.000 ARG A 860 *********************** 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 84 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 1.082 Fit side-chains outliers start: 14 outliers final: 3 residues processed: 83 average time/residue: 0.1778 time to fit residues: 22.8207 Evaluate side-chains 61 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0879 time to fit residues: 1.8846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9293 Z= 0.166 Angle : 0.504 8.267 12636 Z= 0.253 Chirality : 0.038 0.209 1513 Planarity : 0.004 0.049 1541 Dihedral : 7.658 134.858 1352 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.93 % Allowed : 13.93 % 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 (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: 2.40 (0.25), residues: 1145 helix: 2.39 (0.19), residues: 759 sheet: 0.52 (0.61), residues: 69 loop : -0.14 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 980 HIS 0.003 0.001 HIS A1065 PHE 0.013 0.001 PHE A1207 TYR 0.008 0.001 TYR A1205 ARG 0.002 0.000 ARG A 324 *********************** 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 81 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.032 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 81 average time/residue: 0.1946 time to fit residues: 23.4118 Evaluate side-chains 63 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0861 time to fit residues: 1.7068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 ** A1390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 9293 Z= 0.644 Angle : 0.782 12.978 12636 Z= 0.391 Chirality : 0.050 0.216 1513 Planarity : 0.005 0.048 1541 Dihedral : 8.106 145.857 1352 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.44 % Allowed : 15.27 % 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: 1.36 (0.24), residues: 1145 helix: 1.58 (0.18), residues: 759 sheet: -0.00 (0.59), residues: 78 loop : -0.45 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1014 HIS 0.011 0.002 HIS A1001 PHE 0.025 0.002 PHE A1207 TYR 0.021 0.002 TYR A1205 ARG 0.005 0.001 ARG A1457 *********************** 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 73 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.995 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 73 average time/residue: 0.1800 time to fit residues: 20.2457 Evaluate side-chains 65 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0877 time to fit residues: 2.5029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** A1390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9293 Z= 0.183 Angle : 0.526 8.747 12636 Z= 0.265 Chirality : 0.039 0.220 1513 Planarity : 0.004 0.047 1541 Dihedral : 7.745 139.500 1352 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.41 % Allowed : 15.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.25), residues: 1145 helix: 2.15 (0.19), residues: 753 sheet: 0.19 (0.60), residues: 78 loop : -0.24 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 877 HIS 0.004 0.001 HIS A1065 PHE 0.017 0.001 PHE A1207 TYR 0.014 0.001 TYR A1205 ARG 0.003 0.000 ARG A 324 *********************** 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 69 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 1.099 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 68 average time/residue: 0.2055 time to fit residues: 21.0503 Evaluate side-chains 60 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1212 time to fit residues: 1.5531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 104 optimal weight: 3.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- 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** A1390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9293 Z= 0.235 Angle : 0.540 10.082 12636 Z= 0.268 Chirality : 0.040 0.200 1513 Planarity : 0.004 0.046 1541 Dihedral : 7.659 140.288 1352 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.83 % Allowed : 15.48 % 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 (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: 2.17 (0.25), residues: 1145 helix: 2.22 (0.19), residues: 753 sheet: 0.30 (0.60), residues: 78 loop : -0.15 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 877 HIS 0.005 0.001 HIS A1001 PHE 0.021 0.001 PHE A1207 TYR 0.013 0.001 TYR A1126 ARG 0.003 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 71 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 1.020 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.1900 time to fit residues: 20.6203 Evaluate side-chains 63 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0916 time to fit residues: 2.1168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3618 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= 0.198 Angle : 0.523 9.242 12636 Z= 0.261 Chirality : 0.039 0.202 1513 Planarity : 0.004 0.045 1541 Dihedral : 7.533 138.539 1352 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 16.10 % Favored : 83.90 % 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: 2.28 (0.25), residues: 1145 helix: 2.29 (0.19), residues: 753 sheet: 0.41 (0.60), residues: 78 loop : -0.07 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 230 HIS 0.004 0.001 HIS A1001 PHE 0.023 0.001 PHE A1207 TYR 0.014 0.001 TYR A1205 ARG 0.002 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 64 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.952 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1878 time to fit residues: 18.2822 Evaluate side-chains 60 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3668 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= 0.181 Angle : 0.518 9.295 12636 Z= 0.257 Chirality : 0.039 0.200 1513 Planarity : 0.004 0.044 1541 Dihedral : 7.480 137.613 1352 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.31 % Allowed : 16.20 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.25), residues: 1145 helix: 2.34 (0.19), residues: 753 sheet: 0.94 (0.63), residues: 69 loop : -0.05 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1065 PHE 0.021 0.001 PHE A1207 TYR 0.018 0.001 TYR A1126 ARG 0.002 0.000 ARG A 381 ********************** 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 66 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.969 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 66 average time/residue: 0.2005 time to fit residues: 20.0690 Evaluate side-chains 63 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0847 time to fit residues: 1.5885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.123473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.101032 restraints weight = 13202.379| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.14 r_work: 0.3170 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3675 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= 0.181 Angle : 0.518 9.295 12636 Z= 0.257 Chirality : 0.039 0.200 1513 Planarity : 0.004 0.044 1541 Dihedral : 7.480 137.613 1352 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 16.51 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.25), residues: 1145 helix: 2.34 (0.19), residues: 753 sheet: 0.94 (0.63), residues: 69 loop : -0.05 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1065 PHE 0.021 0.001 PHE A1207 TYR 0.018 0.001 TYR A1126 ARG 0.002 0.000 ARG A 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.94 seconds wall clock time: 33 minutes 35.03 seconds (2015.03 seconds total)