Starting phenix.real_space_refine on Thu Mar 14 15:01:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/03_2024/7vlu_32027.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/03_2024/7vlu_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_32027/03_2024/7vlu_32027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/03_2024/7vlu_32027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/03_2024/7vlu_32027.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlu_32027/03_2024/7vlu_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-dev-5265/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: 5.51, 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: 4.05 Conformation dependent library (CDL) restraints added in 1.8 seconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 70.9% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 230 through 241 removed outlier: 4.403A pdb=" N LEU A 234 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N HIS A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 278 removed outlier: 3.765A pdb=" N LYS A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 312 removed outlier: 6.376A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'A' and resid 347 through 393 Processing helix chain 'A' and resid 396 through 402 removed outlier: 4.220A pdb=" N LEU A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 428 removed outlier: 4.683A pdb=" N THR A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 451 through 462 removed outlier: 4.084A pdb=" N VAL A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 498 Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 507 through 557 Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 564 through 584 Proline residue: A 581 - end of helix removed outlier: 4.207A pdb=" N LEU A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 607 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 786 through 791 removed outlier: 3.600A pdb=" N ASP A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 839 through 850 Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.989A pdb=" N ASP A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 875 removed outlier: 3.985A pdb=" N THR A 873 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 899 through 910 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 987 through 1018 removed outlier: 4.031A pdb=" N PHE A 991 " --> pdb=" O PHE A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1074 removed outlier: 3.558A pdb=" N THR A1052 " --> pdb=" O VAL A1048 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A1053 " --> pdb=" O THR A1049 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.633A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1102 removed outlier: 4.083A pdb=" N ILE A1088 " --> pdb=" O PRO A1084 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1176 removed outlier: 4.002A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.922A pdb=" N LYS A1154 " --> pdb=" O ARG A1150 " (cutoff:3.500A) Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1177 through 1184 Processing helix chain 'A' and resid 1186 through 1236 Processing helix chain 'A' and resid 1242 through 1281 removed outlier: 3.513A pdb=" N LEU A1248 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A1253 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A1281 " --> pdb=" O LYS A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1284 No H-bonds generated for 'chain 'A' and resid 1282 through 1284' Processing helix chain 'A' and resid 1347 through 1355 Processing helix chain 'A' and resid 1377 through 1382 Processing helix chain 'A' and resid 1399 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1432 through 1435 removed outlier: 3.771A pdb=" N ASP A1435 " --> pdb=" O GLY A1432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1432 through 1435' Processing helix chain 'A' and resid 1439 through 1443 removed outlier: 3.627A pdb=" N GLU A1443 " --> pdb=" O GLU A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1461 removed outlier: 4.044A pdb=" N ARG A1461 " --> pdb=" O ARG A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1491 Processing helix chain 'A' and resid 1525 through 1532 Processing helix chain 'A' and resid 1535 through 1543 Processing sheet with id=AA1, first strand: chain 'A' and resid 687 through 692 removed outlier: 6.628A pdb=" N ILE A 687 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR A 671 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 689 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS A 669 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 691 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 748 through 751 removed outlier: 6.591A pdb=" N VAL A 829 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL A 865 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 831 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR A 697 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 888 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS A 882 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1331 removed outlier: 6.680A pdb=" N LYS A1326 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N CYS A1314 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL A1328 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE A1310 " --> pdb=" O VAL A1367 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1367 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP A1312 " --> pdb=" O LYS A1365 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A1365 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A1363 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ARG A1316 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE A1361 " --> pdb=" O ARG A1316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1386 through 1388 removed outlier: 6.608A pdb=" N SER A1386 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASP A1469 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE A1388 " --> pdb=" O ASP A1469 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A1466 " --> pdb=" O VAL A1497 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE A1499 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N MET A1468 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY A1339 " --> pdb=" O LEU A1513 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE A1515 " --> pdb=" O GLY A1339 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS A1341 " --> pdb=" O PHE A1515 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A1514 " --> pdb=" O GLU A1522 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A1522 " --> pdb=" O VAL A1514 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER A1516 " --> pdb=" O LEU A1520 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU A1520 " --> pdb=" O SER A1516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1397 through 1398 614 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 4.32 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: 0.330 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: 2.210 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.410 Find NCS groups from input model: 0.250 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: 35.050 ------------------------------------------------------------------------------- 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 : 1.066 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: 0.2476 time to fit residues: 52.4908 Evaluate side-chains 75 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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: 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: 8.9990 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: 0.8271 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9293 Z= 0.332 Angle : 0.654 12.236 12636 Z= 0.325 Chirality : 0.044 0.225 1513 Planarity : 0.005 0.060 1541 Dihedral : 8.793 143.964 1366 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.58 % Allowed : 10.63 % Favored : 86.79 % 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: 0.88 (0.24), residues: 1145 helix: 1.24 (0.18), residues: 765 sheet: -0.54 (0.55), residues: 69 loop : -0.66 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1260 HIS 0.005 0.001 HIS A1065 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 98 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 1.167 Fit side-chains REVERT: A 230 TRP cc_start: 0.6456 (OUTLIER) cc_final: 0.6007 (p-90) REVERT: A 237 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8171 (t) REVERT: A 243 ILE cc_start: 0.8487 (mt) cc_final: 0.8281 (mp) REVERT: A 539 MET cc_start: 0.8075 (mmm) cc_final: 0.7480 (mmm) REVERT: A 888 ARG cc_start: 0.8550 (tpp-160) cc_final: 0.8333 (tpp-160) REVERT: A 910 MET cc_start: 0.8026 (mtp) cc_final: 0.7808 (mtm) REVERT: A 1192 GLN cc_start: 0.8245 (tt0) cc_final: 0.7985 (mt0) REVERT: A 1468 MET cc_start: 0.8927 (mtt) cc_final: 0.8611 (mtp) REVERT: A 1498 THR cc_start: 0.8398 (p) cc_final: 0.8098 (p) outliers start: 25 outliers final: 10 residues processed: 96 average time/residue: 0.2071 time to fit residues: 28.7593 Evaluate side-chains 74 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1379 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9980 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: 4.9990 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9293 Z= 0.228 Angle : 0.549 9.061 12636 Z= 0.275 Chirality : 0.040 0.202 1513 Planarity : 0.004 0.057 1541 Dihedral : 8.231 138.941 1360 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.79 % Allowed : 11.35 % Favored : 85.86 % 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: 1.79 (0.24), residues: 1145 helix: 1.98 (0.18), residues: 765 sheet: -0.18 (0.57), residues: 69 loop : -0.44 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 230 HIS 0.004 0.001 HIS A1065 PHE 0.013 0.001 PHE A1207 TYR 0.011 0.001 TYR A1126 ARG 0.003 0.000 ARG A 381 *********************** 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 105 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 78 time to evaluate : 1.064 Fit side-chains REVERT: A 323 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7519 (tt0) REVERT: A 405 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8459 (ptp) REVERT: A 833 ASP cc_start: 0.8019 (t0) cc_final: 0.7572 (t70) REVERT: A 1192 GLN cc_start: 0.8175 (tt0) cc_final: 0.7930 (mt0) REVERT: A 1434 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8551 (tp) REVERT: A 1468 MET cc_start: 0.8856 (mtt) cc_final: 0.8493 (mtp) REVERT: A 1498 THR cc_start: 0.8421 (p) cc_final: 0.8184 (t) outliers start: 27 outliers final: 10 residues processed: 97 average time/residue: 0.1800 time to fit residues: 26.2435 Evaluate side-chains 77 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 MET 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 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1434 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 chunk 112 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.8223 moved from start: 0.2882 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= 0.175 Angle : 0.524 8.808 12636 Z= 0.259 Chirality : 0.039 0.212 1513 Planarity : 0.004 0.050 1541 Dihedral : 7.947 135.835 1357 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.27 % Allowed : 12.18 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.25), residues: 1145 helix: 2.36 (0.18), residues: 759 sheet: 0.29 (0.60), residues: 69 loop : -0.22 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1214 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A1207 TYR 0.010 0.001 TYR A1205 ARG 0.002 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 98 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 1.131 Fit side-chains REVERT: A 405 MET cc_start: 0.8661 (ptp) cc_final: 0.8433 (ptp) REVERT: A 833 ASP cc_start: 0.8235 (t0) cc_final: 0.8027 (t0) REVERT: A 1192 GLN cc_start: 0.8115 (tt0) cc_final: 0.7895 (mt0) REVERT: A 1434 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8454 (tp) REVERT: A 1468 MET cc_start: 0.8834 (mtt) cc_final: 0.8358 (mtp) REVERT: A 1483 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8582 (tp) REVERT: A 1498 THR cc_start: 0.8537 (p) cc_final: 0.8306 (t) outliers start: 22 outliers final: 11 residues processed: 96 average time/residue: 0.1722 time to fit residues: 25.4113 Evaluate side-chains 74 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 448 LEU 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 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1434 LEU Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9293 Z= 0.275 Angle : 0.563 9.746 12636 Z= 0.279 Chirality : 0.040 0.191 1513 Planarity : 0.004 0.047 1541 Dihedral : 7.959 137.999 1356 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.58 % Allowed : 12.90 % 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 (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: 2.23 (0.25), residues: 1145 helix: 2.25 (0.18), residues: 759 sheet: 0.48 (0.61), residues: 69 loop : -0.17 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 979 HIS 0.005 0.001 HIS A1065 PHE 0.013 0.001 PHE A1207 TYR 0.011 0.001 TYR A1205 ARG 0.002 0.000 ARG A1457 *********************** 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 fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 1.108 Fit side-chains REVERT: A 1192 GLN cc_start: 0.8162 (tt0) cc_final: 0.7873 (mt0) REVERT: A 1434 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8454 (tp) REVERT: A 1468 MET cc_start: 0.8830 (mtt) cc_final: 0.8456 (mtp) REVERT: A 1498 THR cc_start: 0.8519 (p) cc_final: 0.8270 (t) outliers start: 25 outliers final: 20 residues processed: 88 average time/residue: 0.1765 time to fit residues: 23.8701 Evaluate side-chains 80 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 406 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 989 LEU 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 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1434 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3229 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= 0.249 Angle : 0.538 9.148 12636 Z= 0.267 Chirality : 0.040 0.203 1513 Planarity : 0.004 0.045 1541 Dihedral : 7.770 137.084 1354 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.27 % Allowed : 13.62 % Favored : 84.11 % 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: 2.34 (0.25), residues: 1145 helix: 2.31 (0.18), residues: 759 sheet: 0.67 (0.62), residues: 69 loop : -0.12 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1214 HIS 0.005 0.001 HIS A1065 PHE 0.012 0.001 PHE A1207 TYR 0.013 0.001 TYR A1126 ARG 0.003 0.000 ARG A 860 *********************** 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 fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 0.860 Fit side-chains REVERT: A 1192 GLN cc_start: 0.8159 (tt0) cc_final: 0.7854 (mt0) REVERT: A 1434 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8560 (tp) REVERT: A 1468 MET cc_start: 0.8836 (mtt) cc_final: 0.8473 (mtp) outliers start: 22 outliers final: 17 residues processed: 84 average time/residue: 0.1784 time to fit residues: 23.0213 Evaluate side-chains 75 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1434 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3313 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= 0.211 Angle : 0.532 8.785 12636 Z= 0.264 Chirality : 0.039 0.205 1513 Planarity : 0.004 0.043 1541 Dihedral : 7.737 136.509 1354 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.89 % Allowed : 14.04 % Favored : 83.08 % 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: 2.35 (0.19), residues: 759 sheet: 0.78 (0.62), residues: 69 loop : -0.07 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 230 HIS 0.004 0.001 HIS A1065 PHE 0.012 0.001 PHE A1207 TYR 0.016 0.001 TYR A1205 ARG 0.002 0.000 ARG A1382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 61 time to evaluate : 1.001 Fit side-chains REVERT: A 422 MET cc_start: 0.8103 (ttp) cc_final: 0.7870 (ttm) REVERT: A 1192 GLN cc_start: 0.8128 (tt0) cc_final: 0.7810 (mt0) REVERT: A 1434 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8513 (tp) REVERT: A 1468 MET cc_start: 0.8924 (mtt) cc_final: 0.8424 (mtp) outliers start: 28 outliers final: 21 residues processed: 85 average time/residue: 0.1782 time to fit residues: 23.2570 Evaluate side-chains 79 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER 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: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3313 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= 0.211 Angle : 0.532 8.785 12636 Z= 0.264 Chirality : 0.039 0.205 1513 Planarity : 0.004 0.043 1541 Dihedral : 7.737 136.509 1354 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.27 % Allowed : 14.45 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.25), residues: 1145 helix: 2.35 (0.19), residues: 759 sheet: 0.78 (0.62), residues: 69 loop : -0.07 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 230 HIS 0.004 0.001 HIS A1065 PHE 0.012 0.001 PHE A1207 TYR 0.016 0.001 TYR A1205 ARG 0.002 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 79 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.164 Fit side-chains REVERT: A 422 MET cc_start: 0.8112 (ttp) cc_final: 0.7869 (ttm) REVERT: A 1192 GLN cc_start: 0.8131 (tt0) cc_final: 0.7810 (mt0) REVERT: A 1434 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8514 (tp) REVERT: A 1468 MET cc_start: 0.8926 (mtt) cc_final: 0.8423 (mtp) outliers start: 22 outliers final: 21 residues processed: 77 average time/residue: 0.1803 time to fit residues: 21.1182 Evaluate side-chains 79 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER 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: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3319 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= 0.211 Angle : 0.532 8.785 12636 Z= 0.264 Chirality : 0.039 0.205 1513 Planarity : 0.004 0.043 1541 Dihedral : 7.738 136.509 1354 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.27 % Allowed : 14.45 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.25), residues: 1145 helix: 2.35 (0.19), residues: 759 sheet: 0.78 (0.62), residues: 69 loop : -0.07 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 230 HIS 0.004 0.001 HIS A1065 PHE 0.012 0.001 PHE A1207 TYR 0.016 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 79 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 0.999 Fit side-chains REVERT: A 422 MET cc_start: 0.8112 (ttp) cc_final: 0.7870 (ttm) REVERT: A 1192 GLN cc_start: 0.8131 (tt0) cc_final: 0.7810 (mt0) REVERT: A 1434 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8513 (tp) REVERT: A 1468 MET cc_start: 0.8926 (mtt) cc_final: 0.8424 (mtp) outliers start: 22 outliers final: 21 residues processed: 77 average time/residue: 0.1792 time to fit residues: 21.1147 Evaluate side-chains 79 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER 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: 116 random chunks: chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3313 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= 0.211 Angle : 0.532 8.785 12636 Z= 0.264 Chirality : 0.039 0.205 1513 Planarity : 0.004 0.043 1541 Dihedral : 7.737 136.509 1354 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.27 % Allowed : 14.45 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.25), residues: 1145 helix: 2.35 (0.19), residues: 759 sheet: 0.78 (0.62), residues: 69 loop : -0.07 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 230 HIS 0.004 0.001 HIS A1065 PHE 0.012 0.001 PHE A1207 TYR 0.016 0.001 TYR A1205 ARG 0.002 0.000 ARG A1382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.037 Fit side-chains REVERT: A 422 MET cc_start: 0.8112 (ttp) cc_final: 0.7869 (ttm) REVERT: A 1192 GLN cc_start: 0.8131 (tt0) cc_final: 0.7810 (mt0) REVERT: A 1434 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8514 (tp) REVERT: A 1468 MET cc_start: 0.8926 (mtt) cc_final: 0.8423 (mtp) outliers start: 22 outliers final: 21 residues processed: 77 average time/residue: 0.1809 time to fit residues: 21.4479 Evaluate side-chains 79 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1256 ASN Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER 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: 116 random chunks: chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.123932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101687 restraints weight = 13145.403| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.14 r_work: 0.3189 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3434 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= 0.171 Angle : 0.515 8.413 12636 Z= 0.255 Chirality : 0.038 0.203 1513 Planarity : 0.004 0.043 1541 Dihedral : 7.607 134.425 1354 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.17 % Allowed : 14.55 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.25), residues: 1145 helix: 2.50 (0.18), residues: 753 sheet: 0.98 (0.63), residues: 69 loop : -0.03 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 877 HIS 0.004 0.001 HIS A1001 PHE 0.012 0.001 PHE A1207 TYR 0.018 0.001 TYR A1205 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: 1769.08 seconds wall clock time: 32 minutes 42.07 seconds (1962.07 seconds total)