Starting phenix.real_space_refine on Thu Jul 2 17:21:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y1m_33566/07_2026/7y1m_33566.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1m_33566/07_2026/7y1m_33566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7y1m_33566/07_2026/7y1m_33566.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y1m_33566/07_2026/7y1m_33566.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y1m_33566/07_2026/7y1m_33566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1m_33566/07_2026/7y1m_33566.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y1m_33566/07_2026/7y1m_33566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1m_33566/07_2026/7y1m_33566.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.085 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 45 5.16 5 C 5836 2.51 5 N 1494 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8957 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 8864 Classifications: {'peptide': 1166} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 35, 'TRANS': 1130} Chain breaks: 7 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 19, 'ASP:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 227 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'BJX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.19, per 1000 atoms: 0.24 Number of scatterers: 8957 At special positions: 0 Unit cell: (70.89, 105.918, 130.104, 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 45 16.00 P 5 15.00 Mg 2 11.99 O 1575 8.00 N 1494 7.00 C 5836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 320.7 milliseconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 72.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 273 Processing helix chain 'A' and resid 284 through 312 removed outlier: 6.440A 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 312 through 324 removed outlier: 3.962A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.768A pdb=" N GLU A 346 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 394 Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 429 through 449 Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 452 through 462 removed outlier: 4.198A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 497 removed outlier: 3.757A pdb=" N ILE A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 507 through 559 removed outlier: 3.510A pdb=" N THR A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 564 through 607 removed outlier: 4.330A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.422A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 716 Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 773 through 785 Processing helix chain 'A' and resid 786 through 793 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: 3.933A pdb=" N ASP A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 899 through 912 removed outlier: 3.543A pdb=" N LEU A 909 " --> pdb=" O HIS A 905 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 985 removed outlier: 4.189A pdb=" N GLY A 985 " --> pdb=" O TYR A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1017 removed outlier: 4.050A pdb=" N GLU A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1074 Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.723A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1102 removed outlier: 3.664A pdb=" N ILE A1088 " --> pdb=" O PRO A1084 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1176 removed outlier: 4.160A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.657A pdb=" N VAL A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1186 through 1237 Processing helix chain 'A' and resid 1240 through 1283 removed outlier: 3.913A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1298 Processing helix chain 'A' and resid 1301 through 1305 removed outlier: 3.546A pdb=" N GLN A1304 " --> pdb=" O HIS A1301 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A1305 " --> pdb=" O TRP A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1301 through 1305' Processing helix chain 'A' and resid 1347 through 1357 removed outlier: 3.761A pdb=" N LEU A1351 " --> pdb=" O GLY A1347 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A1352 " --> pdb=" O LYS A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1384 Processing helix chain 'A' and resid 1399 through 1404 Processing helix chain 'A' and resid 1410 through 1421 removed outlier: 3.729A pdb=" N LEU A1414 " --> pdb=" O THR A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1432 through 1435 Processing helix chain 'A' and resid 1439 through 1443 removed outlier: 3.856A pdb=" N GLU A1443 " --> pdb=" O GLU A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1462 Processing helix chain 'A' and resid 1476 through 1490 Processing helix chain 'A' and resid 1502 through 1508 removed outlier: 4.276A pdb=" N ILE A1506 " --> pdb=" O ARG A1502 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR A1508 " --> pdb=" O HIS A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 Processing helix chain 'A' and resid 1536 through 1541 Processing sheet with id=AA1, first strand: chain 'A' and resid 690 through 691 removed outlier: 3.717A pdb=" N ILE A 668 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 671 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 724 " --> pdb=" O THR A 671 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 687 removed outlier: 3.611A pdb=" N ASN A 686 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY A 673 " --> pdb=" O ASN A 686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 748 through 751 removed outlier: 6.184A pdb=" N ALA A 749 " --> pdb=" O PHE A 830 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP A 832 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA A 751 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 696 " --> pdb=" O TRP A 877 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE A 879 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET A 698 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N MET A 881 " --> pdb=" O MET A 698 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 700 " --> pdb=" O MET A 881 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1325 through 1332 removed outlier: 5.923A pdb=" N LYS A1326 " --> pdb=" O VAL A1315 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL A1315 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA A1330 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS A1311 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE A1332 " --> pdb=" O LYS A1309 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS A1309 " --> pdb=" O ILE A1332 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A1308 " --> pdb=" O ILE A1368 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE A1368 " --> pdb=" O ILE A1308 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A1310 " --> pdb=" O ILE A1366 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A1366 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP A1312 " --> pdb=" O GLY A1364 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A1364 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS A1314 " --> pdb=" O PHE A1362 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1386 through 1388 removed outlier: 6.487A pdb=" N SER A1386 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASP A1469 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A1388 " --> pdb=" O ASP A1469 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A1466 " --> pdb=" O VAL A1497 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE A1499 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET A1468 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A1511 " --> pdb=" O LYS A1337 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS A1341 " --> pdb=" O ILE A1513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1397 through 1398 631 hydrogen bonds defined for protein. 1857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1371 1.31 - 1.43: 2421 1.43 - 1.56: 5262 1.56 - 1.68: 16 1.68 - 1.81: 72 Bond restraints: 9142 Sorted by residual: bond pdb=" C16 BJX A1604 " pdb=" N1 BJX A1604 " ideal model delta sigma weight residual 1.344 1.449 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" CA GLN A 323 " pdb=" C GLN A 323 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.27e-02 6.20e+03 2.58e+01 bond pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 1.524 1.575 -0.051 1.22e-02 6.72e+03 1.76e+01 bond pdb=" CA GLY A 320 " pdb=" C GLY A 320 " ideal model delta sigma weight residual 1.516 1.559 -0.043 1.09e-02 8.42e+03 1.54e+01 bond pdb=" CA VAL A 322 " pdb=" C VAL A 322 " ideal model delta sigma weight residual 1.523 1.573 -0.049 1.27e-02 6.20e+03 1.50e+01 ... (remaining 9137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 12242 1.56 - 3.12: 141 3.12 - 4.68: 46 4.68 - 6.24: 16 6.24 - 7.81: 5 Bond angle restraints: 12450 Sorted by residual: angle pdb=" C ILE A 321 " pdb=" CA ILE A 321 " pdb=" CB ILE A 321 " ideal model delta sigma weight residual 111.97 105.44 6.53 1.28e+00 6.10e-01 2.60e+01 angle pdb=" C VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 112.14 105.83 6.31 1.35e+00 5.49e-01 2.18e+01 angle pdb=" N VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 110.54 115.92 -5.38 1.36e+00 5.41e-01 1.56e+01 angle pdb=" N GLN A 323 " pdb=" CA GLN A 323 " pdb=" CB GLN A 323 " ideal model delta sigma weight residual 110.01 115.58 -5.57 1.45e+00 4.76e-01 1.48e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" CB ILE A 321 " ideal model delta sigma weight residual 110.55 114.76 -4.21 1.17e+00 7.31e-01 1.29e+01 ... (remaining 12445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.81: 5295 31.81 - 63.61: 65 63.61 - 95.42: 4 95.42 - 127.23: 3 127.23 - 159.03: 3 Dihedral angle restraints: 5370 sinusoidal: 1976 harmonic: 3394 Sorted by residual: dihedral pdb=" O1B ADP A1605 " pdb=" O3A ADP A1605 " pdb=" PB ADP A1605 " pdb=" PA ADP A1605 " ideal model delta sinusoidal sigma weight residual 300.00 158.34 141.66 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O2A ADP A1605 " pdb=" O3A ADP A1605 " pdb=" PA ADP A1605 " pdb=" PB ADP A1605 " ideal model delta sinusoidal sigma weight residual -60.00 49.28 -109.28 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" C5' ADP A1605 " pdb=" O5' ADP A1605 " pdb=" PA ADP A1605 " pdb=" O2A ADP A1605 " ideal model delta sinusoidal sigma weight residual -60.00 47.81 -107.80 1 2.00e+01 2.50e-03 3.13e+01 ... (remaining 5367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1365 0.065 - 0.129: 128 0.129 - 0.194: 6 0.194 - 0.258: 2 0.258 - 0.323: 3 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CA ILE A 321 " pdb=" N ILE A 321 " pdb=" C ILE A 321 " pdb=" CB ILE A 321 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2' ATP A1603 " pdb=" C1' ATP A1603 " pdb=" C3' ATP A1603 " pdb=" O2' ATP A1603 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' ATP A1603 " pdb=" C2' ATP A1603 " pdb=" C4' ATP A1603 " pdb=" O3' ATP A1603 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1501 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 580 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 581 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 752 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C ALA A 752 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA A 752 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN A 753 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 505 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C TYR A 505 " -0.022 2.00e-02 2.50e+03 pdb=" O TYR A 505 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA A 506 " 0.008 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1662 2.77 - 3.30: 9507 3.30 - 3.83: 14884 3.83 - 4.37: 16655 4.37 - 4.90: 29806 Nonbonded interactions: 72514 Sorted by model distance: nonbonded pdb="MG MG A1602 " pdb=" O1G ATP A1603 " model vdw 2.234 2.170 nonbonded pdb=" N GLU A 889 " pdb=" OE1 GLU A 889 " model vdw 2.239 3.120 nonbonded pdb=" OG SER A1349 " pdb=" O1A ADP A1605 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A1602 " model vdw 2.284 2.170 nonbonded pdb=" NH1 ARG A1400 " pdb=" OD1 ASP A1435 " model vdw 2.288 3.120 ... (remaining 72509 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 group one per residue 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: 2.170 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 0.105 9142 Z= 0.208 Angle : 0.526 7.805 12450 Z= 0.279 Chirality : 0.040 0.323 1504 Planarity : 0.003 0.053 1513 Dihedral : 11.808 159.034 3170 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.33 % Allowed : 2.74 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.25), residues: 1150 helix: 2.26 (0.19), residues: 790 sheet: 0.77 (0.62), residues: 73 loop : 0.32 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1461 TYR 0.011 0.001 TYR A 505 PHE 0.011 0.001 PHE A1149 TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.21 ( 9142) covalent geometry : angle 0.52636 / 0.28 (12450) hydrogen bonds : bond 0.12350 / 7.70 ( 631) hydrogen bonds : angle 5.19950 / 3.70 ( 1857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7415 (tptt) REVERT: A 284 SER cc_start: 0.8518 (t) cc_final: 0.8231 (m) REVERT: A 351 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7900 (mp) REVERT: A 405 MET cc_start: 0.7217 (mmm) cc_final: 0.6848 (mmt) REVERT: A 687 ILE cc_start: 0.7740 (mt) cc_final: 0.7534 (mt) REVERT: A 698 MET cc_start: 0.8240 (mtm) cc_final: 0.8028 (mtp) REVERT: A 993 MET cc_start: 0.7777 (ttm) cc_final: 0.7556 (ttm) REVERT: A 1083 THR cc_start: 0.9034 (m) cc_final: 0.8528 (p) REVERT: A 1333 LYS cc_start: 0.8363 (mtmm) cc_final: 0.7955 (tmtt) REVERT: A 1445 PHE cc_start: 0.8392 (m-80) cc_final: 0.8150 (m-80) outliers start: 3 outliers final: 0 residues processed: 146 average time/residue: 0.0877 time to fit residues: 18.1186 Evaluate side-chains 104 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 GLN A1028 GLN A1402 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118997 restraints weight = 12987.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118709 restraints weight = 8636.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118561 restraints weight = 7398.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119662 restraints weight = 7467.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119650 restraints weight = 5743.933| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9142 Z= 0.156 Angle : 0.614 10.230 12450 Z= 0.294 Chirality : 0.041 0.172 1504 Planarity : 0.004 0.048 1513 Dihedral : 8.830 143.487 1261 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.43 % Allowed : 8.22 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.24), residues: 1150 helix: 2.25 (0.18), residues: 802 sheet: 0.67 (0.60), residues: 68 loop : 0.52 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1357 TYR 0.016 0.001 TYR A 505 PHE 0.016 0.001 PHE A 552 TRP 0.010 0.001 TRP A 906 HIS 0.005 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 9142) covalent geometry : angle 0.61413 / 0.29 (12450) hydrogen bonds : bond 0.04726 / 3.09 ( 631) hydrogen bonds : angle 4.22730 / 2.96 ( 1857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7403 (tptt) REVERT: A 284 SER cc_start: 0.8694 (t) cc_final: 0.8364 (m) REVERT: A 405 MET cc_start: 0.7003 (mmm) cc_final: 0.6714 (mmt) REVERT: A 539 MET cc_start: 0.8305 (mmt) cc_final: 0.8060 (mmt) REVERT: A 1083 THR cc_start: 0.8830 (m) cc_final: 0.8504 (p) REVERT: A 1123 MET cc_start: 0.8390 (tpp) cc_final: 0.7812 (tpp) REVERT: A 1333 LYS cc_start: 0.8275 (mtmm) cc_final: 0.8007 (tmtt) REVERT: A 1334 PRO cc_start: 0.7725 (Cg_endo) cc_final: 0.6524 (Cg_exo) REVERT: A 1376 LEU cc_start: 0.8668 (mt) cc_final: 0.8443 (mt) REVERT: A 1445 PHE cc_start: 0.8418 (m-80) cc_final: 0.8206 (m-80) outliers start: 13 outliers final: 8 residues processed: 126 average time/residue: 0.0904 time to fit residues: 16.3342 Evaluate side-chains 108 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.147858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113739 restraints weight = 12937.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113652 restraints weight = 9070.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114784 restraints weight = 6842.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115184 restraints weight = 5615.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115399 restraints weight = 5048.052| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9142 Z= 0.207 Angle : 0.614 7.308 12450 Z= 0.295 Chirality : 0.042 0.170 1504 Planarity : 0.004 0.047 1513 Dihedral : 8.422 149.355 1259 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.08 % Allowed : 9.87 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.24), residues: 1150 helix: 2.14 (0.18), residues: 801 sheet: 0.55 (0.60), residues: 71 loop : 0.33 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.019 0.001 TYR A 228 PHE 0.018 0.001 PHE A 552 TRP 0.011 0.001 TRP A1214 HIS 0.006 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 9142) covalent geometry : angle 0.61380 / 0.30 (12450) hydrogen bonds : bond 0.04827 / 3.15 ( 631) hydrogen bonds : angle 4.18196 / 2.94 ( 1857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7402 (tptt) REVERT: A 231 MET cc_start: 0.8452 (tpt) cc_final: 0.8222 (tpt) REVERT: A 239 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.7695 (m90) REVERT: A 284 SER cc_start: 0.8777 (t) cc_final: 0.8396 (m) REVERT: A 405 MET cc_start: 0.7085 (mmm) cc_final: 0.6523 (mmt) REVERT: A 1083 THR cc_start: 0.8830 (m) cc_final: 0.8531 (p) REVERT: A 1123 MET cc_start: 0.8561 (tpp) cc_final: 0.7828 (tpp) REVERT: A 1333 LYS cc_start: 0.8332 (mtmm) cc_final: 0.8015 (tmtt) REVERT: A 1334 PRO cc_start: 0.7786 (Cg_endo) cc_final: 0.6755 (Cg_exo) outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.0914 time to fit residues: 15.7817 Evaluate side-chains 111 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 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 = 0.3767 r_free = 0.3767 target = 0.146386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115358 restraints weight = 13200.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114785 restraints weight = 13277.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115242 restraints weight = 11269.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115551 restraints weight = 10249.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116143 restraints weight = 8304.700| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9142 Z= 0.136 Angle : 0.555 7.976 12450 Z= 0.264 Chirality : 0.039 0.161 1504 Planarity : 0.004 0.043 1513 Dihedral : 8.091 140.389 1259 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.86 % Allowed : 11.73 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.24), residues: 1150 helix: 2.34 (0.18), residues: 799 sheet: 0.73 (0.60), residues: 71 loop : 0.35 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.012 0.001 TYR A 228 PHE 0.014 0.001 PHE A 552 TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9142) covalent geometry : angle 0.55481 / 0.26 (12450) hydrogen bonds : bond 0.04400 / 2.87 ( 631) hydrogen bonds : angle 3.99061 / 2.80 ( 1857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7261 (tptt) REVERT: A 231 MET cc_start: 0.8559 (tpt) cc_final: 0.8276 (tpt) REVERT: A 239 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7426 (m90) REVERT: A 284 SER cc_start: 0.8801 (t) cc_final: 0.8407 (m) REVERT: A 405 MET cc_start: 0.7039 (mmm) cc_final: 0.6483 (mmt) REVERT: A 707 LYS cc_start: 0.8040 (ptpp) cc_final: 0.7821 (mtmm) REVERT: A 1083 THR cc_start: 0.8791 (m) cc_final: 0.8523 (p) REVERT: A 1123 MET cc_start: 0.8501 (tpp) cc_final: 0.7841 (tpp) REVERT: A 1128 THR cc_start: 0.8879 (m) cc_final: 0.8246 (p) REVERT: A 1322 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8078 (tptt) REVERT: A 1334 PRO cc_start: 0.7553 (Cg_endo) cc_final: 0.6569 (Cg_exo) REVERT: A 1376 LEU cc_start: 0.8585 (mt) cc_final: 0.8309 (mt) outliers start: 17 outliers final: 12 residues processed: 125 average time/residue: 0.0882 time to fit residues: 15.9634 Evaluate side-chains 116 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 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 = 0.3773 r_free = 0.3773 target = 0.146955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116123 restraints weight = 13049.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115093 restraints weight = 13498.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116034 restraints weight = 11806.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116428 restraints weight = 9436.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116749 restraints weight = 7933.983| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9142 Z= 0.127 Angle : 0.543 7.896 12450 Z= 0.258 Chirality : 0.039 0.154 1504 Planarity : 0.003 0.043 1513 Dihedral : 7.803 134.791 1259 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.08 % Allowed : 11.84 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.25), residues: 1150 helix: 2.46 (0.18), residues: 799 sheet: 0.90 (0.66), residues: 61 loop : 0.36 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.015 0.001 TYR A 228 PHE 0.013 0.001 PHE A 552 TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9142) covalent geometry : angle 0.54258 / 0.26 (12450) hydrogen bonds : bond 0.04236 / 2.77 ( 631) hydrogen bonds : angle 3.86990 / 2.71 ( 1857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7444 (tptt) REVERT: A 231 MET cc_start: 0.8402 (tpt) cc_final: 0.8175 (tpt) REVERT: A 239 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7329 (m90) REVERT: A 284 SER cc_start: 0.8730 (t) cc_final: 0.8327 (m) REVERT: A 405 MET cc_start: 0.6798 (mmm) cc_final: 0.6516 (mmt) REVERT: A 707 LYS cc_start: 0.7944 (ptpp) cc_final: 0.7641 (mtmm) REVERT: A 1123 MET cc_start: 0.8287 (tpp) cc_final: 0.7653 (tpp) REVERT: A 1128 THR cc_start: 0.8675 (m) cc_final: 0.8148 (p) REVERT: A 1322 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8128 (tptt) outliers start: 19 outliers final: 14 residues processed: 124 average time/residue: 0.0925 time to fit residues: 16.4851 Evaluate side-chains 117 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 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 = 0.3841 r_free = 0.3841 target = 0.151856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119568 restraints weight = 12865.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119220 restraints weight = 9169.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119189 restraints weight = 8480.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119791 restraints weight = 7465.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120277 restraints weight = 6055.964| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9142 Z= 0.121 Angle : 0.540 8.363 12450 Z= 0.255 Chirality : 0.038 0.163 1504 Planarity : 0.003 0.043 1513 Dihedral : 7.529 129.494 1259 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.75 % Allowed : 12.83 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.25), residues: 1150 helix: 2.53 (0.18), residues: 799 sheet: 1.00 (0.66), residues: 61 loop : 0.43 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.014 0.001 TYR A 228 PHE 0.012 0.001 PHE A1453 TRP 0.007 0.001 TRP A1214 HIS 0.003 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9142) covalent geometry : angle 0.54045 / 0.26 (12450) hydrogen bonds : bond 0.04108 / 2.69 ( 631) hydrogen bonds : angle 3.79316 / 2.65 ( 1857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7414 (tptt) REVERT: A 231 MET cc_start: 0.8313 (tpt) cc_final: 0.8080 (tpt) REVERT: A 239 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7180 (m90) REVERT: A 284 SER cc_start: 0.8802 (t) cc_final: 0.8363 (m) REVERT: A 405 MET cc_start: 0.6896 (mmm) cc_final: 0.6591 (mmt) REVERT: A 910 MET cc_start: 0.6021 (mpp) cc_final: 0.5221 (ttt) REVERT: A 1123 MET cc_start: 0.8306 (tpp) cc_final: 0.7730 (tpp) REVERT: A 1128 THR cc_start: 0.8641 (m) cc_final: 0.8226 (p) REVERT: A 1322 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8088 (tptt) REVERT: A 1445 PHE cc_start: 0.8303 (m-80) cc_final: 0.8026 (m-80) outliers start: 16 outliers final: 14 residues processed: 121 average time/residue: 0.0940 time to fit residues: 16.2922 Evaluate side-chains 115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 73 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 81 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.150179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117107 restraints weight = 13017.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116619 restraints weight = 9510.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117413 restraints weight = 7399.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117530 restraints weight = 6756.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118167 restraints weight = 5849.255| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9142 Z= 0.152 Angle : 0.584 12.672 12450 Z= 0.275 Chirality : 0.040 0.234 1504 Planarity : 0.003 0.040 1513 Dihedral : 7.404 133.073 1259 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.08 % Allowed : 12.61 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.25), residues: 1150 helix: 2.42 (0.18), residues: 801 sheet: 1.01 (0.67), residues: 61 loop : 0.48 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.014 0.001 TYR A 228 PHE 0.015 0.001 PHE A 552 TRP 0.008 0.001 TRP A1214 HIS 0.005 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9142) covalent geometry : angle 0.58412 / 0.27 (12450) hydrogen bonds : bond 0.04253 / 2.79 ( 631) hydrogen bonds : angle 3.81572 / 2.67 ( 1857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7424 (tttp) REVERT: A 231 MET cc_start: 0.8356 (tpt) cc_final: 0.8137 (tpt) REVERT: A 239 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7280 (m90) REVERT: A 284 SER cc_start: 0.8792 (t) cc_final: 0.8355 (m) REVERT: A 405 MET cc_start: 0.6916 (mmm) cc_final: 0.6631 (mmt) REVERT: A 520 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7022 (mtp) REVERT: A 910 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5358 (ttt) REVERT: A 1123 MET cc_start: 0.8386 (tpp) cc_final: 0.7721 (tpp) REVERT: A 1128 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8186 (p) REVERT: A 1322 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8061 (tptt) REVERT: A 1445 PHE cc_start: 0.8381 (m-80) cc_final: 0.8127 (m-80) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.0901 time to fit residues: 14.9932 Evaluate side-chains 114 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116594 restraints weight = 12903.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115652 restraints weight = 9355.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116412 restraints weight = 8132.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116970 restraints weight = 6166.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117201 restraints weight = 5539.020| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9142 Z= 0.167 Angle : 0.587 11.038 12450 Z= 0.277 Chirality : 0.040 0.214 1504 Planarity : 0.004 0.042 1513 Dihedral : 7.339 133.808 1259 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.41 % Allowed : 12.72 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.25), residues: 1150 helix: 2.36 (0.18), residues: 803 sheet: 0.99 (0.67), residues: 61 loop : 0.42 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.015 0.001 TYR A 228 PHE 0.016 0.001 PHE A 552 TRP 0.009 0.001 TRP A1214 HIS 0.006 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 9142) covalent geometry : angle 0.58735 / 0.28 (12450) hydrogen bonds : bond 0.04314 / 2.83 ( 631) hydrogen bonds : angle 3.84548 / 2.69 ( 1857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7449 (tttp) REVERT: A 231 MET cc_start: 0.8348 (tpt) cc_final: 0.8121 (tpt) REVERT: A 239 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7143 (m90) REVERT: A 284 SER cc_start: 0.8804 (t) cc_final: 0.8364 (m) REVERT: A 405 MET cc_start: 0.6987 (mmm) cc_final: 0.6416 (mmt) REVERT: A 520 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6980 (mtp) REVERT: A 910 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5351 (ttt) REVERT: A 1123 MET cc_start: 0.8441 (tpp) cc_final: 0.7720 (tpp) REVERT: A 1128 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8183 (p) REVERT: A 1322 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8055 (tptt) outliers start: 22 outliers final: 17 residues processed: 111 average time/residue: 0.0881 time to fit residues: 14.2897 Evaluate side-chains 116 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 ASN A 686 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.150154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117749 restraints weight = 12942.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118449 restraints weight = 9729.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118889 restraints weight = 7951.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119344 restraints weight = 6845.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119436 restraints weight = 5347.639| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9142 Z= 0.153 Angle : 0.572 10.840 12450 Z= 0.270 Chirality : 0.039 0.193 1504 Planarity : 0.004 0.042 1513 Dihedral : 7.229 132.424 1259 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.19 % Allowed : 12.72 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.25), residues: 1150 helix: 2.35 (0.18), residues: 804 sheet: 0.97 (0.67), residues: 61 loop : 0.42 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1091 TYR 0.014 0.001 TYR A 228 PHE 0.034 0.001 PHE A1445 TRP 0.009 0.001 TRP A1214 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9142) covalent geometry : angle 0.57165 / 0.27 (12450) hydrogen bonds : bond 0.04272 / 2.81 ( 631) hydrogen bonds : angle 3.83023 / 2.68 ( 1857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7421 (tttp) REVERT: A 231 MET cc_start: 0.8376 (tpt) cc_final: 0.8142 (tpt) REVERT: A 239 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7058 (m90) REVERT: A 284 SER cc_start: 0.8810 (t) cc_final: 0.8366 (m) REVERT: A 405 MET cc_start: 0.6984 (mmm) cc_final: 0.6411 (mmt) REVERT: A 520 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6983 (mtp) REVERT: A 910 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5376 (ttt) REVERT: A 1123 MET cc_start: 0.8457 (tpp) cc_final: 0.7718 (tpp) REVERT: A 1128 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8221 (p) REVERT: A 1322 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8091 (tptt) outliers start: 20 outliers final: 15 residues processed: 111 average time/residue: 0.0871 time to fit residues: 14.0781 Evaluate side-chains 114 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 ASN A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119014 restraints weight = 12876.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118317 restraints weight = 9611.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119138 restraints weight = 7415.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119219 restraints weight = 6042.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121185 restraints weight = 5506.234| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9142 Z= 0.127 Angle : 0.562 10.685 12450 Z= 0.263 Chirality : 0.039 0.179 1504 Planarity : 0.003 0.042 1513 Dihedral : 7.008 126.585 1259 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.41 % Allowed : 13.16 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.25), residues: 1150 helix: 2.47 (0.18), residues: 804 sheet: 0.93 (0.68), residues: 60 loop : 0.38 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1461 TYR 0.015 0.001 TYR A 505 PHE 0.024 0.001 PHE A1445 TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9142) covalent geometry : angle 0.56206 / 0.26 (12450) hydrogen bonds : bond 0.04085 / 2.69 ( 631) hydrogen bonds : angle 3.75097 / 2.62 ( 1857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7390 (tttp) REVERT: A 239 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.6928 (m90) REVERT: A 284 SER cc_start: 0.8726 (t) cc_final: 0.8303 (m) REVERT: A 405 MET cc_start: 0.6881 (mmm) cc_final: 0.6623 (mmt) REVERT: A 520 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6993 (mtp) REVERT: A 910 MET cc_start: 0.6161 (OUTLIER) cc_final: 0.5428 (ttt) REVERT: A 1123 MET cc_start: 0.8343 (tpp) cc_final: 0.7699 (tpp) REVERT: A 1128 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 1322 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8052 (tptt) outliers start: 22 outliers final: 17 residues processed: 117 average time/residue: 0.0866 time to fit residues: 14.7838 Evaluate side-chains 119 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119611 restraints weight = 12821.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119204 restraints weight = 9792.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119807 restraints weight = 7107.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120121 restraints weight = 6071.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120278 restraints weight = 5647.395| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9142 Z= 0.121 Angle : 0.570 10.906 12450 Z= 0.264 Chirality : 0.039 0.169 1504 Planarity : 0.003 0.043 1513 Dihedral : 6.906 125.659 1259 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.30 % Allowed : 13.38 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.25), residues: 1150 helix: 2.54 (0.18), residues: 802 sheet: 0.80 (0.68), residues: 60 loop : 0.45 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.012 0.001 TYR A 228 PHE 0.026 0.001 PHE A1445 TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9142) covalent geometry : angle 0.56998 / 0.26 (12450) hydrogen bonds : bond 0.04048 / 2.66 ( 631) hydrogen bonds : angle 3.71911 / 2.61 ( 1857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1478.93 seconds wall clock time: 26 minutes 33.63 seconds (1593.63 seconds total)