Starting phenix.real_space_refine on Sun Dec 29 00:39:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1m_33566/12_2024/7y1m_33566.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1m_33566/12_2024/7y1m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1m_33566/12_2024/7y1m_33566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1m_33566/12_2024/7y1m_33566.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1m_33566/12_2024/7y1m_33566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1m_33566/12_2024/7y1m_33566.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 21, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 9} 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: 6.10, per 1000 atoms: 0.68 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: 2.92 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.23 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: 3.23 Time building geometry restraints manager: 3.25 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: 5313 31.81 - 63.61: 81 63.61 - 95.42: 11 95.42 - 127.23: 3 127.23 - 159.03: 3 Dihedral angle restraints: 5411 sinusoidal: 2017 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 5408 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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= 0.222 Angle : 0.526 7.805 12450 Z= 0.279 Chirality : 0.040 0.323 1504 Planarity : 0.003 0.053 1513 Dihedral : 12.727 159.034 3211 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (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 TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 PHE 0.011 0.001 PHE A1149 TYR 0.011 0.001 TYR A 505 ARG 0.002 0.000 ARG A1461 *********************** 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 : 1.006 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: 0.8230 (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: 0.7741 (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: 0.9035 (m) cc_final: 0.8528 (p) REVERT: A 1333 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7955 (tmtt) REVERT: A 1445 PHE cc_start: 0.8392 (m-80) cc_final: 0.8149 (m-80) outliers start: 3 outliers final: 0 residues processed: 146 average time/residue: 0.2212 time to fit residues: 45.5439 Evaluate side-chains 105 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 97 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.0470 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 GLN A1028 GLN A1504 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1173 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= 0.229 Angle : 0.596 10.086 12450 Z= 0.288 Chirality : 0.040 0.174 1504 Planarity : 0.004 0.047 1513 Dihedral : 10.901 141.998 1302 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.32 % Allowed : 8.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.25), residues: 1150 helix: 2.33 (0.18), residues: 801 sheet: 0.70 (0.60), residues: 68 loop : 0.52 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1214 HIS 0.005 0.001 HIS A1001 PHE 0.014 0.001 PHE A 552 TYR 0.016 0.001 TYR A 505 ARG 0.004 0.000 ARG A1357 *********************** 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 128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7413 (tptt) REVERT: A 284 SER cc_start: 0.8723 (t) cc_final: 0.8418 (m) REVERT: A 405 MET cc_start: 0.7197 (mmm) cc_final: 0.6901 (mmt) REVERT: A 1083 THR cc_start: 0.8956 (m) cc_final: 0.8572 (p) REVERT: A 1123 MET cc_start: 0.8431 (tpp) cc_final: 0.7682 (tpp) REVERT: A 1333 LYS cc_start: 0.8376 (mtmm) cc_final: 0.7961 (tmtt) REVERT: A 1334 PRO cc_start: 0.7902 (Cg_endo) cc_final: 0.6635 (Cg_exo) outliers start: 12 outliers final: 7 residues processed: 123 average time/residue: 0.2001 time to fit residues: 35.7513 Evaluate side-chains 109 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1355 PHE 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 58 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9142 Z= 0.284 Angle : 0.603 8.740 12450 Z= 0.289 Chirality : 0.041 0.170 1504 Planarity : 0.004 0.046 1513 Dihedral : 10.377 140.283 1300 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.86 % Allowed : 9.54 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.24), residues: 1150 helix: 2.28 (0.18), residues: 795 sheet: 0.69 (0.60), residues: 69 loop : 0.39 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1214 HIS 0.006 0.001 HIS A1065 PHE 0.017 0.001 PHE A 552 TYR 0.018 0.001 TYR A 228 ARG 0.003 0.000 ARG A1357 *********************** 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 130 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7436 (tptt) REVERT: A 239 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7736 (m90) REVERT: A 284 SER cc_start: 0.8770 (t) cc_final: 0.8388 (m) REVERT: A 405 MET cc_start: 0.7196 (mmm) cc_final: 0.6929 (mmt) REVERT: A 1083 THR cc_start: 0.8862 (m) cc_final: 0.8517 (p) REVERT: A 1123 MET cc_start: 0.8487 (tpp) cc_final: 0.7770 (tpp) REVERT: A 1289 TYR cc_start: 0.7811 (m-80) cc_final: 0.7446 (m-80) REVERT: A 1333 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7955 (tmtt) REVERT: A 1334 PRO cc_start: 0.7866 (Cg_endo) cc_final: 0.6592 (Cg_exo) outliers start: 17 outliers final: 13 residues processed: 124 average time/residue: 0.2242 time to fit residues: 39.2172 Evaluate side-chains 116 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 1162 SER 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 1483 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1833 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= 0.201 Angle : 0.560 8.424 12450 Z= 0.267 Chirality : 0.040 0.171 1504 Planarity : 0.004 0.043 1513 Dihedral : 10.012 130.632 1300 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.97 % Allowed : 10.75 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.25), residues: 1150 helix: 2.39 (0.18), residues: 803 sheet: 0.65 (0.59), residues: 71 loop : 0.43 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 756 HIS 0.004 0.001 HIS A1065 PHE 0.017 0.001 PHE A 854 TYR 0.011 0.001 TYR A 228 ARG 0.002 0.000 ARG A1091 *********************** 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 128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7395 (tptt) REVERT: A 239 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.7489 (m90) REVERT: A 284 SER cc_start: 0.8819 (t) cc_final: 0.8396 (m) REVERT: A 405 MET cc_start: 0.7126 (mmm) cc_final: 0.6853 (mmt) REVERT: A 906 TRP cc_start: 0.8708 (m-10) cc_final: 0.8435 (m-10) REVERT: A 910 MET cc_start: 0.7245 (mpp) cc_final: 0.5649 (ttt) REVERT: A 1083 THR cc_start: 0.8762 (m) cc_final: 0.8501 (p) REVERT: A 1123 MET cc_start: 0.8383 (tpp) cc_final: 0.7759 (tpp) REVERT: A 1128 THR cc_start: 0.8832 (m) cc_final: 0.8218 (p) REVERT: A 1322 LYS cc_start: 0.8671 (ttpt) cc_final: 0.7955 (tptt) REVERT: A 1333 LYS cc_start: 0.8330 (mtmm) cc_final: 0.7947 (tmtt) REVERT: A 1334 PRO cc_start: 0.7776 (Cg_endo) cc_final: 0.6515 (Cg_exo) outliers start: 18 outliers final: 13 residues processed: 122 average time/residue: 0.1999 time to fit residues: 34.9842 Evaluate side-chains 122 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.0010 chunk 100 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2013 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= 0.185 Angle : 0.541 8.278 12450 Z= 0.256 Chirality : 0.039 0.172 1504 Planarity : 0.003 0.043 1513 Dihedral : 9.846 128.333 1300 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.75 % Allowed : 11.51 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.25), residues: 1150 helix: 2.50 (0.18), residues: 803 sheet: 0.85 (0.59), residues: 71 loop : 0.45 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 PHE 0.013 0.001 PHE A1356 TYR 0.016 0.001 TYR A 228 ARG 0.003 0.000 ARG A 774 *********************** 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: 16 poor density : 111 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7408 (tptt) REVERT: A 239 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7289 (m90) REVERT: A 284 SER cc_start: 0.8846 (t) cc_final: 0.8432 (m) REVERT: A 405 MET cc_start: 0.7099 (mmm) cc_final: 0.6825 (mmt) REVERT: A 910 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.5881 (ttt) REVERT: A 1123 MET cc_start: 0.8353 (tpp) cc_final: 0.7767 (tpp) REVERT: A 1128 THR cc_start: 0.8730 (m) cc_final: 0.8194 (p) REVERT: A 1322 LYS cc_start: 0.8685 (ttpt) cc_final: 0.7975 (tptt) REVERT: A 1333 LYS cc_start: 0.8331 (mtmm) cc_final: 0.8032 (tmtt) REVERT: A 1334 PRO cc_start: 0.7709 (Cg_endo) cc_final: 0.6459 (Cg_exo) REVERT: A 1445 PHE cc_start: 0.8502 (m-80) cc_final: 0.8106 (m-80) outliers start: 16 outliers final: 12 residues processed: 123 average time/residue: 0.2114 time to fit residues: 36.8437 Evaluate side-chains 116 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9142 Z= 0.229 Angle : 0.561 8.134 12450 Z= 0.265 Chirality : 0.039 0.162 1504 Planarity : 0.003 0.043 1513 Dihedral : 9.736 130.951 1300 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.74 % Allowed : 11.40 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.24), residues: 1150 helix: 2.40 (0.18), residues: 800 sheet: 0.90 (0.59), residues: 71 loop : 0.42 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1214 HIS 0.005 0.001 HIS A1065 PHE 0.015 0.001 PHE A 552 TYR 0.013 0.001 TYR A 228 ARG 0.002 0.000 ARG A 774 *********************** 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 136 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7445 (tttp) REVERT: A 239 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7269 (m90) REVERT: A 284 SER cc_start: 0.8882 (t) cc_final: 0.8426 (m) REVERT: A 405 MET cc_start: 0.7151 (mmm) cc_final: 0.6860 (mmt) REVERT: A 520 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7090 (mtp) REVERT: A 910 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.5874 (ttt) REVERT: A 1123 MET cc_start: 0.8430 (tpp) cc_final: 0.7737 (tpp) REVERT: A 1128 THR cc_start: 0.8728 (m) cc_final: 0.8201 (p) REVERT: A 1322 LYS cc_start: 0.8685 (ttpt) cc_final: 0.7966 (tptt) REVERT: A 1333 LYS cc_start: 0.8328 (mtmm) cc_final: 0.8028 (tmtt) REVERT: A 1334 PRO cc_start: 0.7700 (Cg_endo) cc_final: 0.6440 (Cg_exo) REVERT: A 1445 PHE cc_start: 0.8529 (m-80) cc_final: 0.8180 (m-80) outliers start: 25 outliers final: 18 residues processed: 128 average time/residue: 0.2111 time to fit residues: 38.4932 Evaluate side-chains 124 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 481 THR 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 1146 GLN Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1302 TRP 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 12 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9142 Z= 0.197 Angle : 0.559 8.335 12450 Z= 0.264 Chirality : 0.039 0.224 1504 Planarity : 0.003 0.043 1513 Dihedral : 9.551 127.038 1300 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.25), residues: 1150 helix: 2.47 (0.18), residues: 804 sheet: 1.03 (0.59), residues: 71 loop : 0.44 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 906 HIS 0.004 0.001 HIS A1065 PHE 0.013 0.001 PHE A 552 TYR 0.014 0.001 TYR A 228 ARG 0.002 0.000 ARG A 774 *********************** 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 128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7423 (tttp) REVERT: A 239 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7096 (m90) REVERT: A 284 SER cc_start: 0.8865 (t) cc_final: 0.8436 (m) REVERT: A 405 MET cc_start: 0.7096 (mmm) cc_final: 0.6816 (mmt) REVERT: A 520 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7075 (mtp) REVERT: A 910 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.5781 (ttt) REVERT: A 1123 MET cc_start: 0.8377 (tpp) cc_final: 0.7751 (tpp) REVERT: A 1128 THR cc_start: 0.8654 (m) cc_final: 0.8212 (p) REVERT: A 1322 LYS cc_start: 0.8692 (ttpt) cc_final: 0.7972 (tptt) REVERT: A 1333 LYS cc_start: 0.8309 (mtmm) cc_final: 0.8025 (tmtt) REVERT: A 1334 PRO cc_start: 0.7656 (Cg_endo) cc_final: 0.6382 (Cg_exo) REVERT: A 1376 LEU cc_start: 0.8590 (mt) cc_final: 0.8206 (mt) REVERT: A 1445 PHE cc_start: 0.8524 (m-80) cc_final: 0.8208 (m-80) outliers start: 19 outliers final: 14 residues processed: 123 average time/residue: 0.2003 time to fit residues: 35.6615 Evaluate side-chains 118 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 481 THR 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 725 VAL Chi-restraints excluded: chain A residue 910 MET 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 1512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2297 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= 0.202 Angle : 0.572 12.444 12450 Z= 0.267 Chirality : 0.039 0.216 1504 Planarity : 0.003 0.042 1513 Dihedral : 9.473 127.273 1300 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.52 % Allowed : 12.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.25), residues: 1150 helix: 2.46 (0.18), residues: 804 sheet: 0.99 (0.59), residues: 72 loop : 0.50 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 906 HIS 0.004 0.001 HIS A1065 PHE 0.013 0.001 PHE A 552 TYR 0.012 0.001 TYR A 228 ARG 0.002 0.000 ARG A 774 *********************** 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 128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7388 (tttp) REVERT: A 239 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7107 (m90) REVERT: A 284 SER cc_start: 0.8871 (t) cc_final: 0.8417 (m) REVERT: A 405 MET cc_start: 0.7061 (mmm) cc_final: 0.6792 (mmt) REVERT: A 520 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7061 (mtp) REVERT: A 910 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.5770 (ttt) REVERT: A 1123 MET cc_start: 0.8389 (tpp) cc_final: 0.7748 (tpp) REVERT: A 1128 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8207 (p) REVERT: A 1322 LYS cc_start: 0.8692 (ttpt) cc_final: 0.7971 (tptt) REVERT: A 1376 LEU cc_start: 0.8621 (mt) cc_final: 0.8229 (mt) outliers start: 23 outliers final: 18 residues processed: 120 average time/residue: 0.2152 time to fit residues: 37.2174 Evaluate side-chains 121 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 481 THR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9142 Z= 0.191 Angle : 0.565 11.732 12450 Z= 0.264 Chirality : 0.039 0.196 1504 Planarity : 0.004 0.082 1513 Dihedral : 9.377 125.747 1300 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.41 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.25), residues: 1150 helix: 2.49 (0.18), residues: 802 sheet: 1.00 (0.59), residues: 71 loop : 0.51 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 906 HIS 0.004 0.001 HIS A1001 PHE 0.037 0.001 PHE A1445 TYR 0.012 0.001 TYR A 505 ARG 0.004 0.000 ARG A1091 *********************** 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 128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7396 (tttp) REVERT: A 239 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7005 (m90) REVERT: A 284 SER cc_start: 0.8857 (t) cc_final: 0.8399 (m) REVERT: A 405 MET cc_start: 0.7131 (mmm) cc_final: 0.6842 (mmt) REVERT: A 520 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7056 (mtp) REVERT: A 910 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.5787 (ttt) REVERT: A 1123 MET cc_start: 0.8373 (tpp) cc_final: 0.7742 (tpp) REVERT: A 1128 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 1322 LYS cc_start: 0.8678 (ttpt) cc_final: 0.7956 (tptt) REVERT: A 1333 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7679 (tmtt) REVERT: A 1376 LEU cc_start: 0.8642 (mt) cc_final: 0.8268 (mt) REVERT: A 1426 MET cc_start: 0.8094 (tpp) cc_final: 0.7805 (tpp) outliers start: 22 outliers final: 16 residues processed: 119 average time/residue: 0.2292 time to fit residues: 39.4594 Evaluate side-chains 121 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 1333 LYS 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 52 optimal weight: 0.0970 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 30.0000 chunk 106 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9142 Z= 0.162 Angle : 0.559 11.594 12450 Z= 0.260 Chirality : 0.038 0.187 1504 Planarity : 0.004 0.041 1513 Dihedral : 9.266 123.099 1300 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.97 % Allowed : 13.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.25), residues: 1150 helix: 2.53 (0.18), residues: 804 sheet: 0.93 (0.59), residues: 71 loop : 0.46 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 906 HIS 0.003 0.000 HIS A1001 PHE 0.027 0.001 PHE A1445 TYR 0.014 0.001 TYR A 505 ARG 0.013 0.000 ARG A1091 ********************** 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 122 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7391 (tttp) REVERT: A 239 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.6921 (m90) REVERT: A 284 SER cc_start: 0.8827 (t) cc_final: 0.8374 (m) REVERT: A 405 MET cc_start: 0.7185 (mmm) cc_final: 0.6895 (mmt) REVERT: A 520 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7066 (mtp) REVERT: A 910 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.5784 (ttt) REVERT: A 1123 MET cc_start: 0.8295 (tpp) cc_final: 0.7695 (tpp) REVERT: A 1128 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8231 (p) REVERT: A 1333 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7726 (tmtt) REVERT: A 1376 LEU cc_start: 0.8612 (mt) cc_final: 0.8168 (mt) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.1989 time to fit residues: 33.4930 Evaluate side-chains 118 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 481 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 725 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 1219 THR Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1437 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3836 r_free = 0.3836 target = 0.151781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119550 restraints weight = 12806.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118330 restraints weight = 9428.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119298 restraints weight = 7029.724| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2480 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= 0.212 Angle : 0.576 11.364 12450 Z= 0.268 Chirality : 0.039 0.174 1504 Planarity : 0.003 0.042 1513 Dihedral : 9.237 126.525 1300 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.19 % Allowed : 13.27 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.25), residues: 1150 helix: 2.46 (0.18), residues: 802 sheet: 0.91 (0.59), residues: 70 loop : 0.47 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 906 HIS 0.005 0.001 HIS A1001 PHE 0.024 0.001 PHE A1445 TYR 0.022 0.001 TYR A 903 ARG 0.010 0.000 ARG A1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.09 seconds wall clock time: 34 minutes 9.58 seconds (2049.58 seconds total)