Starting phenix.real_space_refine on Fri Oct 11 07:50:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2024/7y1m_33566.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2024/7y1m_33566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2024/7y1m_33566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_2024/7y1m_33566.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1m_33566/10_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-5477/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: 6.27, per 1000 atoms: 0.70 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: 2.73 Conformation dependent library (CDL) restraints added in 1.1 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: 1.16 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: 3.76 Time building geometry restraints manager: 3.05 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.250 Find NCS groups from input model: 0.100 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 0.887 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: 0.2186 time to fit residues: 45.0398 Evaluate side-chains 105 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: