Starting phenix.real_space_refine on Sat Dec 28 22:15:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1n_33567/12_2024/7y1n_33567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1n_33567/12_2024/7y1n_33567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1n_33567/12_2024/7y1n_33567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1n_33567/12_2024/7y1n_33567.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1n_33567/12_2024/7y1n_33567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1n_33567/12_2024/7y1n_33567.cif" } resolution = 3.61 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= 0.005 sd= 0.079 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 39 5.16 5 C 5712 2.51 5 N 1467 2.21 5 O 1538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8763 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1171, 8670 Classifications: {'peptide': 1171} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 35, 'TRANS': 1135} Chain breaks: 7 Unresolved non-hydrogen bonds: 571 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 34, 'GLU:plan': 27, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 352 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: 6.02, per 1000 atoms: 0.69 Number of scatterers: 8763 At special positions: 0 Unit cell: (69.222, 95.076, 133.44, 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 39 16.00 P 5 15.00 Mg 2 11.99 O 1538 8.00 N 1467 7.00 C 5712 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: 3.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 72.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 217 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 237 Processing helix chain 'A' and resid 256 through 275 Processing helix chain 'A' and resid 284 through 312 removed outlier: 3.582A pdb=" N ALA A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 6.473A 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 325 removed outlier: 4.176A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 347 through 394 Processing helix chain 'A' and resid 405 through 462 removed outlier: 3.628A pdb=" N GLU A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Proline residue: A 429 - end of helix removed outlier: 3.798A pdb=" N TRP A 432 " --> pdb=" O CYS A 428 " (cutoff:3.500A) Proline residue: A 435 - end of helix removed outlier: 8.338A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N SER A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 498 removed outlier: 3.665A pdb=" N ILE A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 506 removed outlier: 3.501A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 559 Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 564 through 607 removed outlier: 4.290A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.080A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 715 removed outlier: 3.840A pdb=" N LEU A 711 " --> pdb=" O LYS A 707 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 786 through 793 removed outlier: 3.627A pdb=" N ASP A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 824 removed outlier: 3.553A pdb=" N GLN A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 850 removed outlier: 3.509A pdb=" N GLU A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 868 through 875 removed outlier: 3.750A pdb=" N TYR A 871 " --> pdb=" O LYS A 868 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR A 873 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 899 through 911 Processing helix chain 'A' and resid 974 through 985 removed outlier: 4.227A pdb=" N GLY A 985 " --> pdb=" O TYR A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1017 Processing helix chain 'A' and resid 1029 through 1075 removed outlier: 3.807A pdb=" N ASN A1067 " --> pdb=" O ASN A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.881A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1094 removed outlier: 3.647A pdb=" N ILE A1088 " --> pdb=" O PRO A1084 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1176 removed outlier: 4.098A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.632A pdb=" N VAL A1151 " --> pdb=" O LYS A1147 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A1154 " --> pdb=" O ARG A1150 " (cutoff:3.500A) Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1186 through 1236 removed outlier: 3.666A pdb=" N THR A1200 " --> pdb=" O GLU A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1283 removed outlier: 3.639A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1283 " --> pdb=" O ASN A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1355 removed outlier: 4.098A pdb=" N PHE A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1376 No H-bonds generated for 'chain 'A' and resid 1374 through 1376' Processing helix chain 'A' and resid 1377 through 1384 removed outlier: 3.646A pdb=" N ARG A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1439 through 1443 Processing helix chain 'A' and resid 1446 through 1461 removed outlier: 4.001A pdb=" N ARG A1461 " --> pdb=" O ARG A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1491 Processing helix chain 'A' and resid 1502 through 1507 removed outlier: 3.756A pdb=" N LEU A1507 " --> pdb=" O HIS A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1532 removed outlier: 3.540A pdb=" N GLN A1532 " --> pdb=" O SER A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1545 Processing sheet with id=AA1, first strand: chain 'A' and resid 690 through 692 removed outlier: 6.753A pdb=" N ILE A 691 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 687 removed outlier: 5.406A pdb=" N SER A 685 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE A 675 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR A 674 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 748 through 751 removed outlier: 6.482A pdb=" N ALA A 749 " --> pdb=" O PHE A 830 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP A 832 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA A 751 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR A 697 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 696 " --> pdb=" O TRP A 877 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE A 879 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET A 698 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N MET A 881 " --> pdb=" O MET A 698 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL A 700 " --> pdb=" O MET A 881 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 878 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 889 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 880 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1331 through 1332 Processing sheet with id=AA5, first strand: chain 'A' and resid 1313 through 1315 removed outlier: 7.947A pdb=" N VAL A1315 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS A1326 " --> pdb=" O VAL A1315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1386 through 1388 removed outlier: 3.525A pdb=" N SER A1386 " --> pdb=" O ILE A1465 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A1466 " --> pdb=" O VAL A1497 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE A1499 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET A1468 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS A1337 " --> pdb=" O LEU A1511 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A1513 " --> pdb=" O LYS A1337 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY A1339 " --> pdb=" O ILE A1513 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET A1515 " --> pdb=" O GLY A1339 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N CYS A1341 " --> pdb=" O MET A1515 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A1522 " --> pdb=" O VAL A1514 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1397 through 1398 635 hydrogen bonds defined for protein. 1860 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: 3.65 Time building geometry restraints manager: 3.26 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: 1331 1.31 - 1.43: 2415 1.43 - 1.56: 5119 1.56 - 1.68: 15 1.68 - 1.81: 65 Bond restraints: 8945 Sorted by residual: bond pdb=" C4 ATP A3004 " pdb=" C5 ATP A3004 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.85e+01 bond pdb=" C16 BJX A3005 " pdb=" N1 BJX A3005 " ideal model delta sigma weight residual 1.344 1.457 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C5 ATP A3004 " pdb=" C6 ATP A3004 " ideal model delta sigma weight residual 1.409 1.464 -0.055 1.00e-02 1.00e+04 3.03e+01 bond pdb=" C5 ATP A3004 " pdb=" N7 ATP A3004 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" CA TYR A1031 " pdb=" C TYR A1031 " ideal model delta sigma weight residual 1.523 1.591 -0.068 1.30e-02 5.92e+03 2.74e+01 ... (remaining 8940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 12182 4.69 - 9.38: 32 9.38 - 14.06: 0 14.06 - 18.75: 0 18.75 - 23.44: 2 Bond angle restraints: 12216 Sorted by residual: angle pdb=" PB ATP A3004 " pdb=" O3B ATP A3004 " pdb=" PG ATP A3004 " ideal model delta sigma weight residual 139.87 116.43 23.44 1.00e+00 1.00e+00 5.49e+02 angle pdb=" PA ATP A3004 " pdb=" O3A ATP A3004 " pdb=" PB ATP A3004 " ideal model delta sigma weight residual 136.83 115.68 21.15 1.00e+00 1.00e+00 4.47e+02 angle pdb=" C5 ATP A3004 " pdb=" C4 ATP A3004 " pdb=" N3 ATP A3004 " ideal model delta sigma weight residual 126.80 118.33 8.47 1.00e+00 1.00e+00 7.17e+01 angle pdb=" N3 ATP A3004 " pdb=" C4 ATP A3004 " pdb=" N9 ATP A3004 " ideal model delta sigma weight residual 127.04 136.10 -9.06 1.15e+00 7.59e-01 6.23e+01 angle pdb=" C ASN A 399 " pdb=" N LEU A 400 " pdb=" CA LEU A 400 " ideal model delta sigma weight residual 120.28 111.24 9.04 1.34e+00 5.57e-01 4.55e+01 ... (remaining 12211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.12: 5181 32.12 - 64.24: 65 64.24 - 96.36: 6 96.36 - 128.48: 2 128.48 - 160.60: 2 Dihedral angle restraints: 5256 sinusoidal: 1846 harmonic: 3410 Sorted by residual: dihedral pdb=" O1B ADP A3001 " pdb=" O3A ADP A3001 " pdb=" PB ADP A3001 " pdb=" PA ADP A3001 " ideal model delta sinusoidal sigma weight residual 300.00 142.89 157.11 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' ADP A3001 " pdb=" O5' ADP A3001 " pdb=" PA ADP A3001 " pdb=" O2A ADP A3001 " ideal model delta sinusoidal sigma weight residual -60.00 -158.59 98.59 1 2.00e+01 2.50e-03 2.76e+01 dihedral pdb=" O2A ADP A3001 " pdb=" O3A ADP A3001 " pdb=" PA ADP A3001 " pdb=" PB ADP A3001 " ideal model delta sinusoidal sigma weight residual -60.00 -144.53 84.53 1 2.00e+01 2.50e-03 2.17e+01 ... (remaining 5253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1262 0.050 - 0.100: 186 0.100 - 0.150: 42 0.150 - 0.200: 2 0.200 - 0.251: 5 Chirality restraints: 1497 Sorted by residual: chirality pdb=" C1' ATP A3004 " pdb=" C2' ATP A3004 " pdb=" N9 ATP A3004 " pdb=" O4' ATP A3004 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ASN A 399 " pdb=" N ASN A 399 " pdb=" C ASN A 399 " pdb=" CB ASN A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA VAL A 703 " pdb=" N VAL A 703 " pdb=" C VAL A 703 " pdb=" CB VAL A 703 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1494 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 399 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C ASN A 399 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN A 399 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 400 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 707 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LYS A 707 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 707 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 708 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1376 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A1377 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1377 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1377 " -0.025 5.00e-02 4.00e+02 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 134 2.67 - 3.23: 9387 3.23 - 3.79: 14165 3.79 - 4.34: 17459 4.34 - 4.90: 30146 Nonbonded interactions: 71291 Sorted by model distance: nonbonded pdb=" N GLU A 508 " pdb=" OE1 GLU A 508 " model vdw 2.118 3.120 nonbonded pdb=" O ASN A 399 " pdb=" OD1 ASN A 399 " model vdw 2.153 3.040 nonbonded pdb=" O1A ADP A3001 " pdb=" O3B ADP A3001 " model vdw 2.153 3.040 nonbonded pdb=" O2B ATP A3004 " pdb=" O2G ATP A3004 " model vdw 2.161 3.040 nonbonded pdb="MG MG A3003 " pdb=" O3G ATP A3004 " model vdw 2.194 2.170 ... (remaining 71286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.840 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 0.005 0.113 8945 Z= 0.350 Angle : 0.700 23.438 12216 Z= 0.471 Chirality : 0.040 0.251 1497 Planarity : 0.003 0.044 1487 Dihedral : 12.084 160.597 3044 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.30 % Allowed : 3.42 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.25), residues: 1155 helix: 2.35 (0.18), residues: 789 sheet: 0.73 (0.75), residues: 50 loop : -0.21 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1214 HIS 0.005 0.001 HIS A1001 PHE 0.008 0.001 PHE A 552 TYR 0.020 0.001 TYR A1031 ARG 0.003 0.000 ARG A1185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LEU cc_start: 0.8555 (tp) cc_final: 0.8344 (tp) REVERT: A 355 LEU cc_start: 0.9257 (tp) cc_final: 0.9045 (tp) REVERT: A 425 LEU cc_start: 0.9062 (tp) cc_final: 0.8825 (tp) REVERT: A 525 SER cc_start: 0.9181 (m) cc_final: 0.8980 (t) REVERT: A 717 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 719 GLN cc_start: 0.8225 (mt0) cc_final: 0.7917 (mt0) REVERT: A 750 TYR cc_start: 0.9126 (t80) cc_final: 0.8636 (t80) REVERT: A 1011 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9216 (tt) REVERT: A 1173 GLU cc_start: 0.7887 (pt0) cc_final: 0.7686 (pt0) REVERT: A 1426 MET cc_start: 0.7743 (tmm) cc_final: 0.7339 (tmm) outliers start: 11 outliers final: 5 residues processed: 162 average time/residue: 0.2159 time to fit residues: 50.0850 Evaluate side-chains 119 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1185 ARG Chi-restraints excluded: chain A residue 1427 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8945 Z= 0.241 Angle : 0.595 6.677 12216 Z= 0.296 Chirality : 0.041 0.160 1497 Planarity : 0.004 0.045 1487 Dihedral : 11.149 161.471 1316 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.48 % Allowed : 8.85 % Favored : 88.67 % 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: 2.63 (0.25), residues: 1155 helix: 2.55 (0.18), residues: 791 sheet: 0.37 (0.69), residues: 50 loop : -0.14 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1260 HIS 0.004 0.001 HIS A1065 PHE 0.014 0.001 PHE A 835 TYR 0.009 0.001 TYR A 777 ARG 0.005 0.001 ARG A1357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.6933 (mm) REVERT: A 345 LEU cc_start: 0.8498 (tt) cc_final: 0.8237 (tp) REVERT: A 355 LEU cc_start: 0.9200 (tp) cc_final: 0.8993 (tp) REVERT: A 502 LEU cc_start: 0.8923 (mp) cc_final: 0.8718 (mp) REVERT: A 717 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8212 (mm-30) REVERT: A 750 TYR cc_start: 0.9095 (t80) cc_final: 0.8681 (t80) REVERT: A 1011 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9252 (tt) REVERT: A 1173 GLU cc_start: 0.7856 (pt0) cc_final: 0.7632 (pt0) REVERT: A 1426 MET cc_start: 0.7804 (tmm) cc_final: 0.7246 (tmm) outliers start: 21 outliers final: 16 residues processed: 147 average time/residue: 0.1735 time to fit residues: 38.2504 Evaluate side-chains 125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8945 Z= 0.243 Angle : 0.574 9.395 12216 Z= 0.283 Chirality : 0.041 0.160 1497 Planarity : 0.004 0.045 1487 Dihedral : 10.427 164.698 1311 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.31 % Allowed : 10.15 % Favored : 86.54 % 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: 2.62 (0.25), residues: 1155 helix: 2.59 (0.18), residues: 785 sheet: -0.12 (0.63), residues: 55 loop : -0.15 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 756 HIS 0.005 0.001 HIS A1065 PHE 0.013 0.001 PHE A 991 TYR 0.011 0.001 TYR A 777 ARG 0.005 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.6995 (mm) REVERT: A 345 LEU cc_start: 0.8447 (tt) cc_final: 0.8186 (tp) REVERT: A 432 TRP cc_start: 0.7894 (m-90) cc_final: 0.7071 (m100) REVERT: A 717 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8202 (mm-30) REVERT: A 719 GLN cc_start: 0.8352 (mt0) cc_final: 0.7881 (mt0) REVERT: A 750 TYR cc_start: 0.9104 (t80) cc_final: 0.8670 (t80) REVERT: A 870 GLN cc_start: 0.8629 (pt0) cc_final: 0.8424 (pm20) REVERT: A 1011 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9166 (tt) REVERT: A 1403 LEU cc_start: 0.8950 (mm) cc_final: 0.8742 (mt) REVERT: A 1426 MET cc_start: 0.7923 (tmm) cc_final: 0.7256 (tmm) outliers start: 28 outliers final: 21 residues processed: 149 average time/residue: 0.2085 time to fit residues: 46.6647 Evaluate side-chains 133 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 0.0040 chunk 106 optimal weight: 0.0870 chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 overall best weight: 0.7974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8945 Z= 0.184 Angle : 0.544 7.076 12216 Z= 0.269 Chirality : 0.040 0.191 1497 Planarity : 0.003 0.044 1487 Dihedral : 10.041 166.387 1310 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.95 % Allowed : 13.46 % Favored : 83.59 % 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: 2.70 (0.25), residues: 1155 helix: 2.62 (0.18), residues: 789 sheet: 0.14 (0.66), residues: 55 loop : -0.10 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1260 HIS 0.004 0.001 HIS A1065 PHE 0.010 0.001 PHE A 552 TYR 0.008 0.001 TYR A 777 ARG 0.004 0.000 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.6828 (mm) REVERT: A 345 LEU cc_start: 0.8373 (tt) cc_final: 0.8081 (tp) REVERT: A 719 GLN cc_start: 0.8379 (mt0) cc_final: 0.7942 (mt0) REVERT: A 750 TYR cc_start: 0.9118 (t80) cc_final: 0.8668 (t80) REVERT: A 1011 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9128 (tt) REVERT: A 1030 PHE cc_start: 0.8598 (t80) cc_final: 0.8292 (t80) REVERT: A 1426 MET cc_start: 0.7940 (tmm) cc_final: 0.7233 (tmm) outliers start: 25 outliers final: 16 residues processed: 146 average time/residue: 0.1639 time to fit residues: 37.2231 Evaluate side-chains 129 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 101 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8945 Z= 0.182 Angle : 0.545 7.768 12216 Z= 0.267 Chirality : 0.040 0.212 1497 Planarity : 0.003 0.043 1487 Dihedral : 9.675 167.717 1310 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.07 % Allowed : 14.99 % Favored : 81.94 % 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: 2.70 (0.25), residues: 1155 helix: 2.64 (0.18), residues: 790 sheet: 0.07 (0.63), residues: 66 loop : -0.14 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1260 HIS 0.004 0.001 HIS A1065 PHE 0.017 0.001 PHE A 991 TYR 0.007 0.001 TYR A 777 ARG 0.003 0.000 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.6791 (mm) REVERT: A 710 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9140 (tt) REVERT: A 719 GLN cc_start: 0.8338 (mt0) cc_final: 0.7902 (mt0) REVERT: A 750 TYR cc_start: 0.9123 (t80) cc_final: 0.8724 (t80) REVERT: A 1011 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9193 (tt) REVERT: A 1030 PHE cc_start: 0.8518 (t80) cc_final: 0.8194 (t80) REVERT: A 1426 MET cc_start: 0.7963 (tmm) cc_final: 0.7499 (tmm) outliers start: 26 outliers final: 18 residues processed: 143 average time/residue: 0.1645 time to fit residues: 35.6457 Evaluate side-chains 136 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8945 Z= 0.193 Angle : 0.558 8.825 12216 Z= 0.269 Chirality : 0.040 0.225 1497 Planarity : 0.003 0.042 1487 Dihedral : 9.352 167.809 1310 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.31 % Allowed : 15.70 % Favored : 80.99 % 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: 2.71 (0.25), residues: 1155 helix: 2.67 (0.18), residues: 785 sheet: 0.05 (0.63), residues: 66 loop : -0.19 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 PHE 0.019 0.001 PHE A 991 TYR 0.008 0.001 TYR A 777 ARG 0.003 0.000 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.6724 (mm) REVERT: A 425 LEU cc_start: 0.8925 (tp) cc_final: 0.8669 (mp) REVERT: A 432 TRP cc_start: 0.7813 (m-90) cc_final: 0.6959 (m100) REVERT: A 521 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8516 (ttmt) REVERT: A 710 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9118 (tt) REVERT: A 719 GLN cc_start: 0.8338 (mt0) cc_final: 0.7930 (mt0) REVERT: A 750 TYR cc_start: 0.9109 (t80) cc_final: 0.8704 (t80) REVERT: A 870 GLN cc_start: 0.8490 (pt0) cc_final: 0.8269 (pm20) REVERT: A 1011 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9181 (tt) REVERT: A 1030 PHE cc_start: 0.8428 (t80) cc_final: 0.8110 (t80) REVERT: A 1415 TRP cc_start: 0.7881 (m100) cc_final: 0.7657 (m100) REVERT: A 1426 MET cc_start: 0.8002 (tmm) cc_final: 0.7509 (tmm) outliers start: 28 outliers final: 21 residues processed: 149 average time/residue: 0.1772 time to fit residues: 39.0892 Evaluate side-chains 143 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8945 Z= 0.165 Angle : 0.546 8.292 12216 Z= 0.263 Chirality : 0.039 0.269 1497 Planarity : 0.003 0.041 1487 Dihedral : 9.003 167.834 1310 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.31 % Allowed : 15.23 % Favored : 81.46 % 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: 1155 helix: 2.76 (0.18), residues: 789 sheet: 0.09 (0.64), residues: 66 loop : -0.15 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 PHE 0.021 0.001 PHE A 991 TYR 0.006 0.001 TYR A 777 ARG 0.005 0.000 ARG A1357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.6616 (mm) REVERT: A 425 LEU cc_start: 0.8879 (tp) cc_final: 0.8618 (mp) REVERT: A 432 TRP cc_start: 0.7600 (m-90) cc_final: 0.6978 (m100) REVERT: A 521 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8546 (ttmt) REVERT: A 710 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9091 (tt) REVERT: A 719 GLN cc_start: 0.8310 (mt0) cc_final: 0.7932 (mt0) REVERT: A 750 TYR cc_start: 0.9076 (t80) cc_final: 0.8691 (t80) REVERT: A 1011 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9184 (tt) REVERT: A 1030 PHE cc_start: 0.8356 (t80) cc_final: 0.8008 (t80) REVERT: A 1426 MET cc_start: 0.7992 (tmm) cc_final: 0.7487 (tmm) outliers start: 28 outliers final: 17 residues processed: 151 average time/residue: 0.1644 time to fit residues: 37.5925 Evaluate side-chains 137 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 102 optimal weight: 0.0870 chunk 108 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8945 Z= 0.177 Angle : 0.560 8.322 12216 Z= 0.270 Chirality : 0.039 0.240 1497 Planarity : 0.003 0.043 1487 Dihedral : 8.774 166.391 1310 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.31 % Allowed : 16.29 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1155 helix: 2.76 (0.18), residues: 789 sheet: 0.10 (0.64), residues: 66 loop : -0.16 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 PHE 0.023 0.001 PHE A 991 TYR 0.021 0.001 TYR A 871 ARG 0.004 0.000 ARG A1357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.6637 (mm) REVERT: A 425 LEU cc_start: 0.8871 (tp) cc_final: 0.8604 (mp) REVERT: A 432 TRP cc_start: 0.7436 (m-90) cc_final: 0.6932 (m100) REVERT: A 521 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8546 (ttmt) REVERT: A 710 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9082 (tt) REVERT: A 719 GLN cc_start: 0.8369 (mt0) cc_final: 0.8028 (mt0) REVERT: A 750 TYR cc_start: 0.9078 (t80) cc_final: 0.8694 (t80) REVERT: A 1011 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9192 (tt) REVERT: A 1030 PHE cc_start: 0.8273 (t80) cc_final: 0.7915 (t80) REVERT: A 1426 MET cc_start: 0.7931 (tmm) cc_final: 0.7342 (tmm) outliers start: 28 outliers final: 22 residues processed: 142 average time/residue: 0.1600 time to fit residues: 34.5322 Evaluate side-chains 137 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1236 SER Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 0.0670 chunk 108 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 104 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8945 Z= 0.164 Angle : 0.568 12.615 12216 Z= 0.268 Chirality : 0.039 0.277 1497 Planarity : 0.003 0.045 1487 Dihedral : 8.583 165.683 1309 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.83 % Allowed : 16.77 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1155 helix: 2.80 (0.18), residues: 790 sheet: 0.09 (0.64), residues: 67 loop : -0.19 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 423 HIS 0.004 0.001 HIS A1065 PHE 0.023 0.001 PHE A 991 TYR 0.018 0.001 TYR A 871 ARG 0.004 0.000 ARG A1357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.6608 (mm) REVERT: A 425 LEU cc_start: 0.8861 (tp) cc_final: 0.8599 (mp) REVERT: A 432 TRP cc_start: 0.7293 (m-90) cc_final: 0.6927 (m100) REVERT: A 521 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8556 (ttmt) REVERT: A 710 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9069 (tt) REVERT: A 719 GLN cc_start: 0.8373 (mt0) cc_final: 0.8095 (mt0) REVERT: A 750 TYR cc_start: 0.9045 (t80) cc_final: 0.8676 (t80) REVERT: A 1009 TYR cc_start: 0.8688 (t80) cc_final: 0.8419 (t80) REVERT: A 1011 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9157 (tt) REVERT: A 1030 PHE cc_start: 0.8189 (t80) cc_final: 0.7799 (t80) REVERT: A 1426 MET cc_start: 0.8042 (tmm) cc_final: 0.7457 (tmm) outliers start: 24 outliers final: 18 residues processed: 141 average time/residue: 0.1661 time to fit residues: 35.2501 Evaluate side-chains 135 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 56 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8945 Z= 0.178 Angle : 0.573 9.993 12216 Z= 0.273 Chirality : 0.040 0.276 1497 Planarity : 0.003 0.047 1487 Dihedral : 8.455 164.233 1309 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.60 % Allowed : 17.71 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.25), residues: 1155 helix: 2.77 (0.18), residues: 791 sheet: 0.15 (0.64), residues: 67 loop : -0.16 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1214 HIS 0.004 0.001 HIS A1065 PHE 0.009 0.001 PHE A 552 TYR 0.012 0.001 TYR A 777 ARG 0.003 0.000 ARG A1357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.6683 (mm) REVERT: A 432 TRP cc_start: 0.7302 (m-90) cc_final: 0.6931 (m100) REVERT: A 521 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8539 (ttmt) REVERT: A 710 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9067 (tt) REVERT: A 719 GLN cc_start: 0.8386 (mt0) cc_final: 0.8107 (mt0) REVERT: A 750 TYR cc_start: 0.9031 (t80) cc_final: 0.8665 (t80) REVERT: A 1009 TYR cc_start: 0.8685 (t80) cc_final: 0.8414 (t80) REVERT: A 1011 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9212 (tt) REVERT: A 1030 PHE cc_start: 0.8153 (t80) cc_final: 0.7763 (t80) outliers start: 22 outliers final: 19 residues processed: 133 average time/residue: 0.1669 time to fit residues: 34.0419 Evaluate side-chains 137 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115097 restraints weight = 14095.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.118614 restraints weight = 6686.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120923 restraints weight = 4281.478| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8945 Z= 0.192 Angle : 0.582 9.804 12216 Z= 0.275 Chirality : 0.040 0.253 1497 Planarity : 0.003 0.049 1487 Dihedral : 8.380 163.250 1309 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.83 % Allowed : 17.71 % Favored : 79.46 % 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: 2.81 (0.25), residues: 1155 helix: 2.73 (0.18), residues: 791 sheet: 0.15 (0.65), residues: 67 loop : -0.18 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1302 HIS 0.004 0.001 HIS A1065 PHE 0.026 0.001 PHE A 991 TYR 0.016 0.001 TYR A 871 ARG 0.003 0.000 ARG A1357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1864.21 seconds wall clock time: 34 minutes 56.05 seconds (2096.05 seconds total)