Starting phenix.real_space_refine on Sat Aug 23 12:35:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c4v_16430/08_2025/8c4v_16430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4v_16430/08_2025/8c4v_16430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2025/8c4v_16430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2025/8c4v_16430.map" model { file = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2025/8c4v_16430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4v_16430/08_2025/8c4v_16430.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 56 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7318 2.51 5 N 1984 2.21 5 O 2315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11731 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1308, 10536 Classifications: {'peptide': 1308} Link IDs: {'PTRANS': 43, 'TRANS': 1264} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 409 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "V" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} Chain: "P" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.27 Number of scatterers: 11731 At special positions: 0 Unit cell: (97.9, 103.4, 114.4, 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 57 16.00 P 56 15.00 Mg 1 11.99 O 2315 8.00 N 1984 7.00 C 7318 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: 1.07 Conformation dependent library (CDL) restraints added in 535.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 13 sheets defined 58.1% alpha, 12.2% beta 17 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 239 through 253 removed outlier: 3.643A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.803A pdb=" N CYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 328 through 343 removed outlier: 4.092A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.528A pdb=" N PHE A 359 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 429 removed outlier: 3.784A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.510A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 564 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 635 removed outlier: 3.954A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 654 through 674 removed outlier: 4.062A pdb=" N ASN A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.652A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 760 removed outlier: 3.592A pdb=" N LYS A 740 " --> pdb=" O ASN A 736 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.813A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.619A pdb=" N LYS A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.600A pdb=" N ILE A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 858 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 929 through 947 Processing helix chain 'A' and resid 982 through 990 removed outlier: 3.772A pdb=" N ARG A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.559A pdb=" N PHE A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A1044 " --> pdb=" O PHE A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1084 Processing helix chain 'A' and resid 1113 through 1127 Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.925A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1192 Processing helix chain 'A' and resid 1200 through 1211 Processing helix chain 'A' and resid 1212 through 1219 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1254 removed outlier: 3.953A pdb=" N TYR A1253 " --> pdb=" O HIS A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1298 removed outlier: 3.829A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A1295 " --> pdb=" O ARG A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1319 Processing helix chain 'A' and resid 1347 through 1351 removed outlier: 4.286A pdb=" N ASP A1351 " --> pdb=" O GLU A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 removed outlier: 3.557A pdb=" N ASP A1369 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 3.859A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1396 Processing helix chain 'A' and resid 1400 through 1411 removed outlier: 3.818A pdb=" N LYS A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1440 Processing helix chain 'A' and resid 1445 through 1453 Processing helix chain 'A' and resid 1465 through 1470 Processing helix chain 'A' and resid 1505 through 1511 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1527 through 1529 No H-bonds generated for 'chain 'A' and resid 1527 through 1529' Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.548A pdb=" N THR A1537 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1565 removed outlier: 3.524A pdb=" N ARG A1558 " --> pdb=" O ASP A1554 " (cutoff:3.500A) Proline residue: A1561 - end of helix removed outlier: 3.704A pdb=" N LYS A1565 " --> pdb=" O PRO A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1592 removed outlier: 3.571A pdb=" N CYS A1586 " --> pdb=" O ALA A1582 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.692A pdb=" N THR A1163 " --> pdb=" O SER A 970 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.692A pdb=" N THR A1163 " --> pdb=" O SER A 970 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 removed outlier: 4.721A pdb=" N THR A 529 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.561A pdb=" N ILE A 562 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA8, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.664A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 893 through 897 removed outlier: 4.065A pdb=" N ALA A 877 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1168 through 1171 Processing sheet with id=AB2, first strand: chain 'A' and resid 1337 through 1338 removed outlier: 4.748A pdb=" N GLN A1337 " --> pdb=" O ARG A1418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1474 through 1479 removed outlier: 4.090A pdb=" N ASP A1474 " --> pdb=" O ARG A1600 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A1600 " --> pdb=" O ASP A1474 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1485 through 1490 584 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1752 1.29 - 1.43: 3543 1.43 - 1.56: 6605 1.56 - 1.69: 107 1.69 - 1.82: 96 Bond restraints: 12103 Sorted by residual: bond pdb=" C SER A 309 " pdb=" O SER A 309 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.17e-02 7.31e+03 3.79e+01 bond pdb=" C ARG A 904 " pdb=" O ARG A 904 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.16e-02 7.43e+03 3.19e+01 bond pdb=" C GLN A 460 " pdb=" O GLN A 460 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.15e-02 7.56e+03 3.17e+01 bond pdb=" C PRO A1222 " pdb=" O PRO A1222 " ideal model delta sigma weight residual 1.237 1.169 0.069 1.26e-02 6.30e+03 2.98e+01 bond pdb=" C LEU A 463 " pdb=" O LEU A 463 " ideal model delta sigma weight residual 1.235 1.170 0.065 1.26e-02 6.30e+03 2.66e+01 ... (remaining 12098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 15847 2.36 - 4.72: 646 4.72 - 7.07: 98 7.07 - 9.43: 21 9.43 - 11.79: 3 Bond angle restraints: 16615 Sorted by residual: angle pdb=" N ARG A 627 " pdb=" CA ARG A 627 " pdb=" C ARG A 627 " ideal model delta sigma weight residual 113.28 102.14 11.14 1.22e+00 6.72e-01 8.34e+01 angle pdb=" C LYS A 287 " pdb=" CA LYS A 287 " pdb=" CB LYS A 287 " ideal model delta sigma weight residual 110.17 102.54 7.63 9.90e-01 1.02e+00 5.93e+01 angle pdb=" N TYR A 628 " pdb=" CA TYR A 628 " pdb=" C TYR A 628 " ideal model delta sigma weight residual 113.41 105.25 8.16 1.22e+00 6.72e-01 4.47e+01 angle pdb=" CA PHE A 291 " pdb=" CB PHE A 291 " pdb=" CG PHE A 291 " ideal model delta sigma weight residual 113.80 120.48 -6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" N LEU A 731 " pdb=" CA LEU A 731 " pdb=" C LEU A 731 " ideal model delta sigma weight residual 113.02 105.11 7.91 1.20e+00 6.94e-01 4.35e+01 ... (remaining 16610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 6899 35.46 - 70.93: 362 70.93 - 106.39: 27 106.39 - 141.85: 1 141.85 - 177.32: 4 Dihedral angle restraints: 7293 sinusoidal: 3447 harmonic: 3846 Sorted by residual: dihedral pdb=" O4' U H 7 " pdb=" C1' U H 7 " pdb=" N1 U H 7 " pdb=" C2 U H 7 " ideal model delta sinusoidal sigma weight residual 200.00 39.39 160.61 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' C S 23 " pdb=" C1' C S 23 " pdb=" N1 C S 23 " pdb=" C2 C S 23 " ideal model delta sinusoidal sigma weight residual 232.00 54.68 177.32 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C H 13 " pdb=" C1' C H 13 " pdb=" N1 C H 13 " pdb=" C2 C H 13 " ideal model delta sinusoidal sigma weight residual 232.00 55.62 176.38 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1782 0.133 - 0.266: 99 0.266 - 0.399: 14 0.399 - 0.533: 1 0.533 - 0.666: 1 Chirality restraints: 1897 Sorted by residual: chirality pdb=" CA THR A1242 " pdb=" N THR A1242 " pdb=" C THR A1242 " pdb=" CB THR A1242 " both_signs ideal model delta sigma weight residual False 2.53 1.86 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA PHE A1132 " pdb=" N PHE A1132 " pdb=" C PHE A1132 " pdb=" CB PHE A1132 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA VAL A1574 " pdb=" N VAL A1574 " pdb=" C VAL A1574 " pdb=" CB VAL A1574 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 1894 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A1212 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C CYS A1212 " -0.073 2.00e-02 2.50e+03 pdb=" O CYS A1212 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL A1213 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 873 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C ARG A 873 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG A 873 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 874 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 459 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C THR A 459 " -0.048 2.00e-02 2.50e+03 pdb=" O THR A 459 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN A 460 " 0.016 2.00e-02 2.50e+03 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 64 2.53 - 3.12: 8964 3.12 - 3.71: 20140 3.71 - 4.31: 29583 4.31 - 4.90: 47571 Nonbonded interactions: 106322 Sorted by model distance: nonbonded pdb=" OD1 ASP A1099 " pdb="MG MG A2201 " model vdw 1.935 2.170 nonbonded pdb=" OG1 THR A 328 " pdb=" OG1 THR A 545 " model vdw 2.216 3.040 nonbonded pdb=" O ASP A 549 " pdb=" OG SER A 552 " model vdw 2.251 3.040 nonbonded pdb=" O ARG A 714 " pdb=" OG SER A 718 " model vdw 2.255 3.040 nonbonded pdb=" O THR A 421 " pdb=" OG SER A 425 " model vdw 2.266 3.040 ... (remaining 106317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.260 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.007 0.076 12103 Z= 0.479 Angle : 1.008 11.791 16615 Z= 0.677 Chirality : 0.067 0.666 1897 Planarity : 0.005 0.062 1890 Dihedral : 19.433 177.318 4803 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.51 % Allowed : 24.72 % Favored : 72.77 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.23), residues: 1294 helix: 0.43 (0.19), residues: 682 sheet: -1.67 (0.47), residues: 104 loop : -1.37 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 880 TYR 0.027 0.002 TYR A1104 PHE 0.042 0.002 PHE A 291 TRP 0.028 0.002 TRP A1131 HIS 0.008 0.001 HIS A1130 Details of bonding type rmsd covalent geometry : bond 0.00704 (12103) covalent geometry : angle 1.00832 (16615) hydrogen bonds : bond 0.16604 ( 609) hydrogen bonds : angle 7.04952 ( 1755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.482 Fit side-chains REVERT: A 452 ASP cc_start: 0.6388 (t0) cc_final: 0.6152 (t0) REVERT: A 461 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8206 (ttmm) REVERT: A 1000 LYS cc_start: 0.8210 (mttt) cc_final: 0.7836 (mttt) REVERT: A 1414 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8031 (mtm) outliers start: 29 outliers final: 14 residues processed: 194 average time/residue: 0.1267 time to fit residues: 35.0237 Evaluate side-chains 175 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1417 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 999 ASN ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 GLN A1324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.169592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.137589 restraints weight = 12818.714| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.27 r_work: 0.3382 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12103 Z= 0.151 Angle : 0.556 6.892 16615 Z= 0.290 Chirality : 0.038 0.197 1897 Planarity : 0.004 0.035 1890 Dihedral : 16.964 177.323 2276 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.63 % Allowed : 23.34 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.23), residues: 1294 helix: 1.07 (0.19), residues: 701 sheet: -1.46 (0.49), residues: 100 loop : -1.26 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1300 TYR 0.013 0.001 TYR A1106 PHE 0.017 0.001 PHE A1143 TRP 0.012 0.001 TRP A 976 HIS 0.006 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00334 (12103) covalent geometry : angle 0.55576 (16615) hydrogen bonds : bond 0.04114 ( 609) hydrogen bonds : angle 4.93365 ( 1755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.426 Fit side-chains REVERT: A 816 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7868 (m-40) REVERT: A 931 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7770 (mttp) REVERT: A 941 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7966 (ptpt) REVERT: A 1000 LYS cc_start: 0.8245 (mttt) cc_final: 0.7915 (mttt) REVERT: A 1119 PHE cc_start: 0.7906 (t80) cc_final: 0.7643 (t80) REVERT: A 1275 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7013 (tm-30) REVERT: A 1276 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7978 (mt) REVERT: A 1283 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.5923 (mpt) REVERT: A 1346 GLU cc_start: 0.7433 (tp30) cc_final: 0.7213 (tp30) REVERT: A 1414 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.6969 (mtm) outliers start: 42 outliers final: 20 residues processed: 219 average time/residue: 0.1243 time to fit residues: 38.5491 Evaluate side-chains 196 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1550 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.168882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.137081 restraints weight = 12829.043| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.26 r_work: 0.3361 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12103 Z= 0.165 Angle : 0.544 7.016 16615 Z= 0.281 Chirality : 0.039 0.184 1897 Planarity : 0.003 0.036 1890 Dihedral : 16.756 179.230 2265 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.15 % Allowed : 22.56 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.23), residues: 1294 helix: 1.16 (0.19), residues: 700 sheet: -1.40 (0.49), residues: 100 loop : -1.19 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 873 TYR 0.013 0.001 TYR A 912 PHE 0.018 0.002 PHE A1357 TRP 0.012 0.001 TRP A 473 HIS 0.004 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00372 (12103) covalent geometry : angle 0.54445 (16615) hydrogen bonds : bond 0.03855 ( 609) hydrogen bonds : angle 4.77022 ( 1755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.447 Fit side-chains REVERT: A 351 ASN cc_start: 0.7570 (m-40) cc_final: 0.7363 (m-40) REVERT: A 744 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: A 755 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.6829 (mtmt) REVERT: A 782 GLN cc_start: 0.8890 (mt0) cc_final: 0.8566 (mt0) REVERT: A 931 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7651 (mttp) REVERT: A 941 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7977 (ptpt) REVERT: A 1000 LYS cc_start: 0.8268 (mttt) cc_final: 0.8054 (mttt) REVERT: A 1119 PHE cc_start: 0.8034 (t80) cc_final: 0.7731 (t80) REVERT: A 1275 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6727 (tm-30) REVERT: A 1276 LEU cc_start: 0.8331 (mt) cc_final: 0.7957 (mt) REVERT: A 1283 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.5893 (mpt) REVERT: A 1403 GLN cc_start: 0.7246 (mt0) cc_final: 0.6903 (mt0) REVERT: A 1414 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.6835 (mtm) REVERT: A 1562 MET cc_start: 0.7155 (ptp) cc_final: 0.6853 (mtm) outliers start: 48 outliers final: 29 residues processed: 215 average time/residue: 0.1276 time to fit residues: 39.0074 Evaluate side-chains 209 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1443 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.169894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.138230 restraints weight = 12782.578| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.27 r_work: 0.3373 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12103 Z= 0.145 Angle : 0.524 6.781 16615 Z= 0.270 Chirality : 0.038 0.178 1897 Planarity : 0.003 0.035 1890 Dihedral : 16.728 179.054 2262 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.49 % Allowed : 22.64 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.23), residues: 1294 helix: 1.27 (0.19), residues: 705 sheet: -1.18 (0.50), residues: 99 loop : -1.16 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 873 TYR 0.017 0.001 TYR A 353 PHE 0.020 0.001 PHE A1357 TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00326 (12103) covalent geometry : angle 0.52393 (16615) hydrogen bonds : bond 0.03639 ( 609) hydrogen bonds : angle 4.59952 ( 1755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.459 Fit side-chains REVERT: A 744 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: A 755 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.6834 (mtmt) REVERT: A 782 GLN cc_start: 0.8879 (mt0) cc_final: 0.8540 (mt0) REVERT: A 931 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7682 (mttp) REVERT: A 941 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7958 (ptpt) REVERT: A 1119 PHE cc_start: 0.8013 (t80) cc_final: 0.7726 (t80) REVERT: A 1275 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6822 (tm-30) REVERT: A 1283 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.5859 (mpt) REVERT: A 1403 GLN cc_start: 0.7217 (mt0) cc_final: 0.6876 (mt0) REVERT: A 1414 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.6750 (mtm) REVERT: A 1562 MET cc_start: 0.7168 (ptp) cc_final: 0.6823 (mtm) outliers start: 52 outliers final: 31 residues processed: 223 average time/residue: 0.1231 time to fit residues: 39.4407 Evaluate side-chains 212 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 HIS ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.171172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139789 restraints weight = 12826.894| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.26 r_work: 0.3409 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12103 Z= 0.126 Angle : 0.515 6.671 16615 Z= 0.264 Chirality : 0.038 0.185 1897 Planarity : 0.003 0.034 1890 Dihedral : 16.648 177.025 2262 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.58 % Allowed : 23.08 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.23), residues: 1294 helix: 1.37 (0.19), residues: 709 sheet: -0.95 (0.51), residues: 97 loop : -1.19 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 873 TYR 0.019 0.001 TYR A 353 PHE 0.020 0.001 PHE A1357 TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00280 (12103) covalent geometry : angle 0.51460 (16615) hydrogen bonds : bond 0.03469 ( 609) hydrogen bonds : angle 4.46782 ( 1755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 0.447 Fit side-chains REVERT: A 479 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8798 (mm) REVERT: A 704 PHE cc_start: 0.7807 (t80) cc_final: 0.7559 (t80) REVERT: A 744 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: A 755 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.6803 (mtmt) REVERT: A 782 GLN cc_start: 0.8849 (mt0) cc_final: 0.8502 (mt0) REVERT: A 864 SER cc_start: 0.8294 (p) cc_final: 0.7973 (t) REVERT: A 874 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: A 931 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7705 (mttp) REVERT: A 941 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7938 (ptpt) REVERT: A 986 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7867 (mtp180) REVERT: A 1119 PHE cc_start: 0.8003 (t80) cc_final: 0.7733 (t80) REVERT: A 1275 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6961 (tm-30) REVERT: A 1283 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.5860 (mpt) REVERT: A 1322 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.4295 (t80) REVERT: A 1414 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.6901 (mtm) REVERT: A 1562 MET cc_start: 0.7191 (ptp) cc_final: 0.6871 (mtm) outliers start: 53 outliers final: 29 residues processed: 224 average time/residue: 0.1207 time to fit residues: 38.7149 Evaluate side-chains 215 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 65 optimal weight: 0.0060 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 0.0020 chunk 74 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 70 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1060 ASN ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.183873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.154794 restraints weight = 12705.011| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.27 r_work: 0.3613 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12103 Z= 0.107 Angle : 0.497 6.855 16615 Z= 0.254 Chirality : 0.037 0.193 1897 Planarity : 0.003 0.033 1890 Dihedral : 16.521 174.742 2259 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.80 % Allowed : 23.68 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.23), residues: 1294 helix: 1.53 (0.20), residues: 711 sheet: -0.79 (0.52), residues: 99 loop : -1.16 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 873 TYR 0.018 0.001 TYR A 912 PHE 0.021 0.001 PHE A1357 TRP 0.012 0.001 TRP A 473 HIS 0.002 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00232 (12103) covalent geometry : angle 0.49658 (16615) hydrogen bonds : bond 0.03307 ( 609) hydrogen bonds : angle 4.36122 ( 1755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.470 Fit side-chains REVERT: A 462 TYR cc_start: 0.8102 (m-80) cc_final: 0.7682 (m-80) REVERT: A 479 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8783 (mm) REVERT: A 755 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.6905 (mtmt) REVERT: A 770 MET cc_start: 0.7984 (tpp) cc_final: 0.7760 (mmm) REVERT: A 782 GLN cc_start: 0.8824 (mt0) cc_final: 0.8475 (mt0) REVERT: A 864 SER cc_start: 0.8141 (p) cc_final: 0.7939 (t) REVERT: A 874 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 931 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7815 (mttp) REVERT: A 941 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7760 (ttpt) REVERT: A 1119 PHE cc_start: 0.8053 (t80) cc_final: 0.7810 (t80) REVERT: A 1276 LEU cc_start: 0.8257 (mt) cc_final: 0.7939 (mt) REVERT: A 1283 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.5883 (mpt) REVERT: A 1322 PHE cc_start: 0.5401 (OUTLIER) cc_final: 0.4615 (t80) REVERT: A 1414 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7070 (mtm) REVERT: A 1559 ILE cc_start: 0.8310 (mt) cc_final: 0.8053 (tp) REVERT: A 1562 MET cc_start: 0.7221 (ptp) cc_final: 0.6898 (mtm) outliers start: 44 outliers final: 30 residues processed: 223 average time/residue: 0.1150 time to fit residues: 37.0771 Evaluate side-chains 218 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1514 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 GLN ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.178720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.146596 restraints weight = 12678.080| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.32 r_work: 0.3543 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12103 Z= 0.178 Angle : 0.546 7.730 16615 Z= 0.280 Chirality : 0.039 0.200 1897 Planarity : 0.004 0.034 1890 Dihedral : 16.503 176.365 2259 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.93 % Allowed : 23.16 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.23), residues: 1294 helix: 1.41 (0.19), residues: 705 sheet: -1.01 (0.49), residues: 99 loop : -1.13 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1300 TYR 0.022 0.001 TYR A 353 PHE 0.020 0.002 PHE A1357 TRP 0.013 0.001 TRP A 473 HIS 0.004 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00405 (12103) covalent geometry : angle 0.54572 (16615) hydrogen bonds : bond 0.03662 ( 609) hydrogen bonds : angle 4.52368 ( 1755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.429 Fit side-chains REVERT: A 462 TYR cc_start: 0.8236 (m-80) cc_final: 0.7603 (m-80) REVERT: A 744 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: A 782 GLN cc_start: 0.8919 (mt0) cc_final: 0.8644 (mt0) REVERT: A 864 SER cc_start: 0.8249 (p) cc_final: 0.7966 (t) REVERT: A 874 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: A 931 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7810 (mttp) REVERT: A 941 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7903 (ptpt) REVERT: A 986 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.7904 (mtp180) REVERT: A 1119 PHE cc_start: 0.8052 (t80) cc_final: 0.7805 (t80) REVERT: A 1276 LEU cc_start: 0.8311 (mt) cc_final: 0.7918 (mt) REVERT: A 1283 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.5923 (mpt) REVERT: A 1322 PHE cc_start: 0.5506 (OUTLIER) cc_final: 0.4658 (t80) REVERT: A 1403 GLN cc_start: 0.7311 (mt0) cc_final: 0.7081 (mt0) REVERT: A 1414 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7076 (mtm) REVERT: A 1562 MET cc_start: 0.7239 (ptp) cc_final: 0.6946 (mtm) outliers start: 57 outliers final: 37 residues processed: 223 average time/residue: 0.1183 time to fit residues: 37.7886 Evaluate side-chains 223 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1053 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1414 MET Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.182196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150852 restraints weight = 12615.995| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.30 r_work: 0.3566 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12103 Z= 0.141 Angle : 0.526 9.085 16615 Z= 0.269 Chirality : 0.038 0.190 1897 Planarity : 0.003 0.036 1890 Dihedral : 16.492 174.945 2259 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.58 % Allowed : 23.94 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.23), residues: 1294 helix: 1.43 (0.19), residues: 706 sheet: -0.93 (0.50), residues: 101 loop : -1.16 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 873 TYR 0.018 0.001 TYR A 353 PHE 0.021 0.002 PHE A1357 TRP 0.012 0.001 TRP A 473 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00316 (12103) covalent geometry : angle 0.52610 (16615) hydrogen bonds : bond 0.03504 ( 609) hydrogen bonds : angle 4.45817 ( 1755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 182 time to evaluate : 0.483 Fit side-chains REVERT: A 462 TYR cc_start: 0.8214 (m-80) cc_final: 0.7619 (m-80) REVERT: A 704 PHE cc_start: 0.7871 (t80) cc_final: 0.7602 (t80) REVERT: A 744 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: A 755 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.6904 (mtmt) REVERT: A 782 GLN cc_start: 0.8884 (mt0) cc_final: 0.8526 (mt0) REVERT: A 874 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7016 (pm20) REVERT: A 931 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7821 (mttp) REVERT: A 941 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7868 (ptpt) REVERT: A 986 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7918 (mtp180) REVERT: A 1119 PHE cc_start: 0.8068 (t80) cc_final: 0.7800 (t80) REVERT: A 1276 LEU cc_start: 0.8259 (mt) cc_final: 0.7913 (mt) REVERT: A 1283 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.5900 (mpt) REVERT: A 1322 PHE cc_start: 0.5436 (OUTLIER) cc_final: 0.4490 (t80) REVERT: A 1562 MET cc_start: 0.7285 (ptp) cc_final: 0.6998 (ptp) outliers start: 53 outliers final: 39 residues processed: 219 average time/residue: 0.1172 time to fit residues: 36.7979 Evaluate side-chains 223 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 105 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 55 optimal weight: 0.0570 chunk 91 optimal weight: 0.9980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.186255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.156310 restraints weight = 12446.950| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.24 r_work: 0.3570 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12103 Z= 0.134 Angle : 0.528 11.160 16615 Z= 0.269 Chirality : 0.038 0.186 1897 Planarity : 0.003 0.041 1890 Dihedral : 16.402 174.407 2256 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.49 % Allowed : 24.20 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.23), residues: 1294 helix: 1.41 (0.19), residues: 708 sheet: -0.85 (0.51), residues: 99 loop : -1.21 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 880 TYR 0.016 0.001 TYR A 353 PHE 0.021 0.002 PHE A1357 TRP 0.012 0.001 TRP A 473 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00302 (12103) covalent geometry : angle 0.52791 (16615) hydrogen bonds : bond 0.03471 ( 609) hydrogen bonds : angle 4.45365 ( 1755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.337 Fit side-chains REVERT: A 462 TYR cc_start: 0.8112 (m-80) cc_final: 0.7669 (m-80) REVERT: A 704 PHE cc_start: 0.7815 (t80) cc_final: 0.7545 (t80) REVERT: A 744 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: A 755 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.6899 (mtmt) REVERT: A 782 GLN cc_start: 0.8875 (mt0) cc_final: 0.8514 (mt0) REVERT: A 864 SER cc_start: 0.8207 (p) cc_final: 0.7938 (t) REVERT: A 874 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: A 880 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.8002 (ttp80) REVERT: A 906 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 931 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7648 (mttp) REVERT: A 941 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7893 (ptpt) REVERT: A 986 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7871 (mtp180) REVERT: A 1119 PHE cc_start: 0.8026 (t80) cc_final: 0.7778 (t80) REVERT: A 1276 LEU cc_start: 0.8213 (mt) cc_final: 0.7869 (mt) REVERT: A 1283 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.5882 (mpt) REVERT: A 1322 PHE cc_start: 0.5351 (OUTLIER) cc_final: 0.4310 (t80) REVERT: A 1562 MET cc_start: 0.7276 (ptp) cc_final: 0.6987 (ptp) outliers start: 52 outliers final: 38 residues processed: 217 average time/residue: 0.1167 time to fit residues: 36.1805 Evaluate side-chains 226 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 96 optimal weight: 0.0010 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.180853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.148971 restraints weight = 12751.299| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.33 r_work: 0.3569 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12103 Z= 0.140 Angle : 0.540 11.121 16615 Z= 0.273 Chirality : 0.039 0.186 1897 Planarity : 0.003 0.040 1890 Dihedral : 16.383 174.504 2256 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.15 % Allowed : 24.72 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.23), residues: 1294 helix: 1.41 (0.19), residues: 706 sheet: -0.88 (0.51), residues: 99 loop : -1.16 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 880 TYR 0.016 0.001 TYR A 353 PHE 0.021 0.002 PHE A1357 TRP 0.012 0.001 TRP A 473 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00317 (12103) covalent geometry : angle 0.53985 (16615) hydrogen bonds : bond 0.03518 ( 609) hydrogen bonds : angle 4.47886 ( 1755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.457 Fit side-chains REVERT: A 349 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6305 (mmt) REVERT: A 462 TYR cc_start: 0.8140 (m-80) cc_final: 0.7676 (m-80) REVERT: A 704 PHE cc_start: 0.7873 (t80) cc_final: 0.7608 (t80) REVERT: A 744 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: A 755 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.6895 (mtmt) REVERT: A 782 GLN cc_start: 0.8886 (mt0) cc_final: 0.8522 (mt0) REVERT: A 864 SER cc_start: 0.8204 (p) cc_final: 0.7940 (t) REVERT: A 874 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: A 931 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7607 (mttp) REVERT: A 941 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7893 (ptpt) REVERT: A 986 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.7877 (mtp180) REVERT: A 1119 PHE cc_start: 0.8019 (t80) cc_final: 0.7773 (t80) REVERT: A 1276 LEU cc_start: 0.8218 (mt) cc_final: 0.7891 (mt) REVERT: A 1283 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.5865 (mpt) REVERT: A 1322 PHE cc_start: 0.5080 (OUTLIER) cc_final: 0.3867 (t80) REVERT: A 1562 MET cc_start: 0.7233 (ptp) cc_final: 0.6931 (ptp) outliers start: 48 outliers final: 37 residues processed: 214 average time/residue: 0.1234 time to fit residues: 37.6519 Evaluate side-chains 225 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 816 ASN Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 903 CYS Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 941 LYS Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 986 ARG Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1179 CYS Chi-restraints excluded: chain A residue 1182 SER Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1322 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1443 THR Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 0.0010 chunk 62 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.181372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151502 restraints weight = 12741.505| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.33 r_work: 0.3584 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12103 Z= 0.133 Angle : 0.543 13.217 16615 Z= 0.273 Chirality : 0.039 0.184 1897 Planarity : 0.003 0.034 1890 Dihedral : 16.363 173.920 2256 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.98 % Allowed : 24.72 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.23), residues: 1294 helix: 1.43 (0.20), residues: 706 sheet: -0.85 (0.51), residues: 99 loop : -1.17 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 873 TYR 0.016 0.001 TYR A1106 PHE 0.023 0.002 PHE A1357 TRP 0.012 0.001 TRP A 473 HIS 0.003 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00299 (12103) covalent geometry : angle 0.54275 (16615) hydrogen bonds : bond 0.03481 ( 609) hydrogen bonds : angle 4.46408 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3060.74 seconds wall clock time: 53 minutes 30.84 seconds (3210.84 seconds total)